https://pages.htgaa.org/2026a/vithushan-varatharaj/homework/week-04-hw-protein-design-part-i/index.htmlPart A: Question 1: How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) To understand this its important to know that elements on the scale of amino acids masses are measured in units of Daltons, defined as the mass of 1/12th of a carbon atom or 1x10^-24 grams. So in 500 grams of meat where following that there is 26 grams of protein per 100g of meat there is then 130 grams of protein. This means there is 130 x 1.67 x 10^-24 daltons of protein (hence amino acids). And since 1 amino acid is on average 100 Daltons we just have to divide by 100 to get the number of amino acid molecules present which ends up to be: 2.171 x 10^24 molecules of amino acids Question 2: Why do humans eat beef but do not become a cow, eat fish but do not become fish? This is because we have enzymes that cleave the proteins we eat into their individual amino acids, these amino acids are then used to build the human into its own unique structures and uses. The protein of each animal consumed isnt "directly transferred" into the human but its broken down into its amino acid constituents, carbohydrate sources etc.. which are then used as the building material. What decides how an organism looks or functions is to do with their genetic coding in their DNA, So the DNA acts as the building instructions and food/protein/amino acids consumed act as the raw mateerials used to carry out these nstructions. Question 3: Why are there only 20 natural amino acids? I Initially thought this was because a limitation in the triplet codon but then i remembered thats 4C3 which is 64 different combinations and they all only end up giving 20 different amino acids which is why they are degenerate. So I assume the reason theres only 20 amino acids in nature is because of a natural selection process that has occured throughout evolution as a combination of what amino acids provided useful and allowed for better survival. Question 4 : Can you make other non-natural amino acids? Design some new amino acids Yes this is possible - non-natural amino acids better known as noncanonical amino acids are those containing side chains beyond the side chains that DNA can code for. By modifying the side chains of the basic glycine-derived α-amino acid structure, more complex functional groups can be introduced to design non-natural amino acids. These include D-amino acids, β-amino acids, and amino acids with modified side chains. Such modifications are crucial in biotechnology and pharmaceuticals for applications including the development of more stable therapeutic peptides, protein engineering, and the study of protein structure and function. Noncanonical amino acids are commonly used to improve the stability of therapeutic peptides by reducing their susceptibility to proteolytic degradation. Proteases recognise specific sequence motifs and backbone geometries, so introducing a non-natural amino acid near a known cleavage site can disrupt this recognition. One effective strategy is the incorporation of D-amino acids, which have the same side chain but opposite stereochemistry to naturally occurring L-amino acids, making them poorly recognised by most proteases. For example, glucagon-like peptide-1 (GLP-1) is rapidly cleaved by DPP-4 at the Ala8–Glu9 bond. Replacing the alanine at position 8 with a D-amino acid such as D-alanine alters the local stereochemistry, reducing enzymatic cleavage and improving peptide half-life while maintaining biological function. Question 5 : Where did amino acids come from before enzymes that make them, and before life started? There are several proposed explanations for how amino acids formed before the origin of life. One key idea is that amino acids were produced through abiotic chemical reactions on early Earth. The early atmosphere is thought to have contained simple gases such as methane (CH₄), ammonia (NH₃), and water vapour (H₂O). With energy sources such as lightning and ultraviolet radiation, these gases could undergo chemical reactions to form organic molecules, including amino acids. This was demonstrated by the Miller-Urey experiment, which successfully produced amino acids under simulated early Earth conditions. In addition, evidence from extraterrestrial sources supports this idea. The Murchison meteorite, which fell in 1969, was found to contain a wide range of organic molecules, including amino acids. This shows that amino acids can form in space and may have been delivered to early Earth via meteorites, contributing to the prebiotic chemical pool from which life eventually emerged. Question 6: If you make an α-helix using D-amino acids, what handedness (right or left) would you expect? Amino acids are chiral and exhibit stereospecificity, meaning their three-dimensional arrangement determines how they interact and fold. Natural proteins are composed of L-amino acids, which form right-handed α-helices due to the specific geometry of the peptide backbone and side chain orientation. If D-amino acids are used instead, the stereochemistry is inverted, resulting in a mirror-image structure. Consequently, D-amino acids form left-handed α-helices, as the backbone geometry and hydrogen bonding pattern are reversed. Question 7: Can you discover additional helices in proteins? The α-helix is one of the most common protein secondary structures, characterised by a right-handed coil with approximately 3.6 amino acid residues per turn. It has a pitch of 5.4 Å and a rise of 1.5 Å per residue, and is stabilised by hydrogen bonds between the carbonyl oxygen of residue i and the amide hydrogen of residue i+4. In principle, other helical structures can exist by altering the number of residues per turn or the hydrogen bonding pattern, such as the 3₁₀ helix (i → i+3) or π-helix (i → i+5), and even left-handed helices under certain conditions. However, the formation of helices in nature is constrained by backbone geometry and energetic stability. Only specific hydrogen bonding patterns and torsional angles are energetically favourable, meaning that while alternative helices are theoretically possible, only a limited number form stable and commonly observed structures in proteins. Question 9: Why do β-sheets tend to aggregate? What is the driving force for β-sheet aggregation? The main idea is that the forces are more stabilised when these sheets aggregate, stacking and slotting into one another. The β-sheets tend to aggregate because their extended backbone structure allows for extensive intermolecular hydrogen bonding between neighbouring strands or sheets. In addition, hydrophobic side chains can align and interact between sheets, further stabilising aggregation. This combination of backbone hydrogen bonding and hydrophobic interactions leads to the formation of highly stable, stacked β-sheet structures, such as those found in amyloid fibrils. Question 10: Why do amyloid diseases form B-sheets? Amyloid diseases arise when normally soluble proteins misfold into structures rich in β-sheets. These β-sheets form highly stable aggregates due to extensive intermolecular hydrogen bonding and hydrophobic interactions. The sheets stack to form insoluble fibrils with a characteristic cross-β structure. These fibrils accumulate in tissues, where they disrupt cellular function and become toxic, ultimately leading to tissue damage and disease. Part B: Protein Analysis and Visualization Hemoglobin is a well-studied and highly important protein found in red blood cells, where it functions as the primary carrier of oxygen throughout the body. It has a quaternary structure composed of four subunits (two α and two β chains), each containing a heme group capable of binding oxygen. Its structure is particularly interesting because it exhibits allosteric, cooperative binding, meaning that the binding of one oxygen molecule increases the affinity for subsequent oxygen molecules, enabling efficient oxygen uptake in the lungs and release in tissues. Since its a quarternary structure of 4 subunits, the alpha and beta chains have two different respective amnino acid sequences. α: VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF DLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLR VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTS KYR β: MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESF GDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSEL HCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGV ANALAHKYH The structure of Hemoglobin can be found on the RCSB Protein Data Bank (e.g. PDB ID: 1A3N). It was first solved in the 1960s–1970s, with modern structures having a resolution of around 2.7 Å, indicating good quality as lower resolution values correspond to more precise structural detail. The solved structure contains not only the protein itself but also additional molecules such as heme groups with Fe²⁺ ions, which are essential for oxygen binding, as well as ligands like oxygen or water molecules. Hemoglobin belongs to the globin protein family, which is characterised by predominantly α-helical structures and a conserved heme-binding pocket. I then uploaded Haemoglobins PDB file to pymol and rendered the following structure visualising it as a cartoon: And then the following two renderings are the same structure but visualised as a ribbon and Ball-and-stick representation:Hugoen