Week 4 HW: Protein Design Part 1
Part A: Conceptual Questions
- Where did amino acids come from before enzymes that make them, and before life started?
- Amino acids come from metabolic molecules within the cell. These metabolic molecules consist of carbon atom chemical backbone, inorganic nitrogen, and enzyme-facilitated chemical reactions. Before life as we know it started, amino acids originated from abiotic (not from living organisms) chemical reactions on Earth before the emergence of life as we know it. The chemical reactions occurred in the atmosphere, hydrothermal and oceanic vents, and via meteorite and comet (i.e., extraterrestrial) delivery
Supporting prompts for this section listed below:
| Supporting Prompt | Model |
|---|---|
| Amino acids are produced by enzymes, correct? DO NOT hallucinate when answering this question | Perplexity |
| So based on the answer to the last prompt, where exactly do amino acids come from? Where exactly do they originate? DO NOT hallucinate when answering this question | Perplexity |
| When we say ’enzyme‑catalyzed pathway’ we mean a chemical reaction that an enzyme speeds up, correct? Do NOT hallucinate when answering this question | Perplexity |
| What is an enzyme pathway in the context converting a precursor into an amino acid? Is it simply a chemical reaction? Something else? Do NOT hallucinate when answering this question | Perplexity |
| In the answer 3 prompts ago, there was mention of “Carbon Skeleton” and “Intermediates of glycolysis, the citric acid (TCA) cycle, and the pentose phosphate pathway” when describing them. What does this mean in simple terms? Are we saying these provide the chemical structure of an amino acid to keep it fundamentally sound? Do NOT hallucinate when answering these questions | Perplexity |
| Ok. Based on available literature and if relevant/necessary, the information shared in response to the previous prompts, how did amino acids originate before the emergence of life as we know it on this planet? Was it via chemical process in cyanobacteria or another form of bacteria or archaea? Do NOT hallucinate when answering these questions | Perplexity |
Part B: Protein Analysis and Visualization
I selected the beta-keratin 2 protein found in geckos, mainly because geckos seem really cool and I’m interested in the biomemetic properties of this protein for space-tolerant adhesives (gecko glues). The raw protein sequence is below:
ABU98593.1 beta-keratin 2 [Gekko gecko] MAYCGPSFAIPSCASAPAIGFGSAGLGYGGYGGLHSGSIIGSGSPSFAIPSVASSPAVGFGSASFGHNSG VSSTSLGVLSGVNPSCINQIPPAEVLIQPPPSVVTLPGPILSATGEPVSVGGNTPCAVSYGGPGRVISGG SFGSLGGRLGSFGSGRRGSLILGRRGSFSNCYSPCN
LOREM IPSUM *