BIO3 - Proteins Flashcards
What are the favourable and unfavourable interactions and energetic
contributions that determine protein folding?
The primary unfavorable force is entropy. The unfolded protein has way more degrees of freedom (calculated as S = K_b*log(omega), where omega is the number of possible conformations/links, in the power of the number of amino acids) and hence is a entropically speaking favored state. The favorable forces/interactions must overcome this unfavorable interaction for the protein to fold.
Hydrophobic effects. Hydrophobic molecules tend to cluster together in an aqueous solution, since the water has more degrees of freedom (higher entropy) when it is not isolating these molecules. For proteins this means that hydrophobic segments of the protein will bind, which is a favorable force for protein folding (i.e. hydrophobic amino acid residues are buried in the core of the protein, resulting in a more stable configuration.
Hydrogen bonds occur between the amino (NH) groups and carboxyl (CO) groups of the amino acids. An individual hydrogen bond contributes favorable with around 20-25 kj/mol. However, since the amino acids also make hydrogen bonds with water (unfolded state) the number of hydrogen bonds before and after folding is approximately the same.
Furthermore ionic interactions (saltbridges), vdW interactions (attractions between closely packed atoms) and aromatic interactions (interactions between aromatic rings) help stabilize the protein.
What are intrinsically disordered proteins?
Intrinsically disordered proteins, are proteins that do not (necessarily) fold
IDPs are associated with signaling and regulatory processes. IDPs can have many different binding partners, and often fold upon binding
What are examples of protein misfolding/aggregation diseases?
Alzheimers, Parkinsons, Huntingtons etc.
What is allostery?
Allostery is a mechanism within proteins, that enforce changes in a region of a proteins because of a binding on another region of the protein (allostery site). This effect is extremely important for e.g. enzymatic function.
What are enzymes and in what ways are they superior to non-biological
catalysts?
Enzymes are proteins that act as biological catalysts, converting substrate(s) into product(s). They provide a high level of specificity for different substrates, and exhibit high kinetic control, which means that reactions rates are enhanced greatly.
The non-biological counterparts are often not as specific, which means that they can require favorable conditions to work as effectively.
What is directed evolution and how is it used to improve enzymes?
Directed evolution of enzymes is controlled mutation, where you (for each mutation/iteration) test the changes in functionality of the enzyme. This way you can increase thermal stability, binding affinity, and catalytic activity on natural and non-natural substrates, or you can make the enzyme catalyze a new reaction.
What are antibodies and what are their roles in biology and their applications?
Antibodies are large glycoproteins (proteins with sugars attached) that can interact with molecular signatures on the surfaces of pathogens. After attachment to pathogens, the immune system can recognize the pathogens and dispose of them.
What are nanobodies and why are they better suited for some applications than
classical antibodies?
Nanobodies are small (single domain) versions of antibodies, found in the immune system of cameloid species. Because of their small size, they can be better suited for some medical applications.
What is the key idea of protein display technologies, such as phage display?
The key concept is to insert a protein-encoding gene into a bacteriophage. This will then result in the bacteriophage expressing this protein on its surface. You now do this with many different protein-encoding genes, and thereby create a “library” of bacteriophages that express different proteins on their surfaces.
You can then expose this library to a particular ligand of interest. After exposure, the proteins with affinity for the ligand will be bound, and you can isolate the proteins of interest. These can then be amplified.
What are these protein display technologies mostly used for?
Phage display is widely used for testing of antibodies (could be in relation to vaccine development). The gene sections that you insert in the bacteriophages will then code for a specific antibody. You can then test the affinity between your library of antibodies and a specific pathogen.
What is proteomics and what experimental method is it mostly based on?
Proteomics is the study of the human proteome (i.e. what proteins (and proteoforms) are expressed in the human organism. The most used method is Mass Spectrometry
What are the advantages and disadvantages of chemical synthesis and
recombinant production of proteins?
In theory chemical synthesis of proteins could be a very good way to find new proteins. However, it is quite difficult to do so. As of now chemical synthesis is limited to peptides and small proteins
Recombinant production of protein utilizes a GMO’d host organism (such as bacteria) to express proteins from an introduced DNA sequence. This makes it easier to produce larger proteins, and to do so at scale, but has certain limitations imposed by the restrictions of the host cell.
What is self-assembly and what is its role in biology? Be able to give some
examples for structures that form through self-assembly.
Self-assembly is the ability of a compound to form without interference. Proteins are an example of this, but so are viruses. Viruses self-assemble based on the proteins that are expressed in the host-cell.
Be able to give some examples for sustainable sourcing of food proteins.
meat cell cultures
recombinantly produced animal protein from microorganisms
fungal proteins (mycoproteins)
insect protein
