Drawing a Peptide: Videos & Practice Problems

To draw a peptide based on its primary structure, we follow a systematic approach that involves three key steps. The first step is to establish the peptide backbone by identifying the nitrogen-carbon-carbon (NCC) sets for each amino acid residue. For a peptide with four amino acids, we will have four NCC sets. Each NCC set consists of a nitrogen atom (N), an alpha carbon (C_α), and a carbon atom (C). The alpha carbon is the central carbon in each NCC set, and we label it accordingly. The terminal ends of the peptide will feature a free amino group (NH₃⁺) at the N-terminus and a free carboxylate group (COO^-) at the C-terminus.

In the second step, we incorporate carbonyl groups (C=O) on the carbon atoms that are not designated as alpha carbons. It is essential to consider the chirality of the amino acids, as life predominantly utilizes L-amino acids. The configuration of the alpha carbon can be determined by the orientation of the R group: if the R group points upwards, it is represented with a wedge, and if it points downwards, it is represented with a dash.

Finally, in the third step, we add hydrogen atoms to the nitrogen atoms and draw the specific R groups for each amino acid. For aspartic acid, the R group is a carboxylic acid (–COOH), which is represented as a carboxylate (–COO^-) in its ionized form. Arginine features a complex R group with a three-carbon backbone and a guanidinium group, characterized by a triangular nitrogen structure. Alanine has a simple methyl group (–CH₃), while tryptophan consists of a five-membered ring connected to a six-membered benzene ring, with a nitrogen atom positioned appropriately to avoid overlap with the benzene structure.

By following these steps, we can accurately depict the peptide structure corresponding to the sequence of amino acids, ensuring that all functional groups and stereochemical configurations are correctly represented.

To draw the chemical structure of the peptide "STRIDE," we follow a systematic approach that involves three key steps. The first step is to establish the peptide backbone and identify the alpha carbons. Each amino acid residue in the peptide contributes a nitrogen-carbon-carbon (NCC) set to the backbone. Since "STRIDE" consists of six amino acid residues, we will have six NCC sets. This means we will draw a sequence of nitrogen and carbon atoms, ensuring that each NCC set is represented. The alpha carbon is the central carbon in each NCC set, and for our peptide, we will identify six alpha carbons, confirming that we have accounted for all six amino acids.

Next, we need to consider the terminal groups. At the N-terminus, there will be a free amino group (NH₃⁺), while at the C-terminus, there will be a free carboxylate group (COO^-). The second step involves adding carbonyl groups to the backbone, which are located on the carbons that are not alpha carbons. Additionally, we must consider the chirality of the amino acids. In biological systems, L-amino acids are predominantly used. The configuration can be determined by the orientation of the R group: if it points up, it is represented with a wedge, and if it points down, it is represented with a dash.

In the final step, we fill in the hydrogen atoms on the nitrogen atoms and add the R groups for each amino acid. The amino acids in "STRIDE" are as follows:

• S for Serine (Ser): The structure includes a hydroxyl group (-OH) attached to the carbon backbone.
• T for Threonine (Thr): This amino acid has a hydroxyl group and a methyl group attached to its central carbon.
• R for Arginine (Arg): Arginine features a three-carbon chain leading to a guanidinium group, which includes a nitrogen structure with a positive charge.
• I for Isoleucine (Ile): Isoleucine is an isomer of leucine, characterized by a branched structure with a methyl group.
• V for Valine (Val): Valine has a V-shaped structure with two methyl groups branching off the central carbon.
• E for Glutamic Acid (Glu): Glutamic acid has an additional methylene group compared to aspartic acid, along with a carboxylate group, making it ionized as glutamate.

By accurately drawing the backbone, identifying the alpha carbons, adding the carbonyl groups, and incorporating the R groups, we successfully construct the complete chemical structure of the peptide "STRIDE." This process highlights the importance of understanding amino acid structures and their configurations in peptide formation.

To draw a peptide consisting of seven amino acid residues, we follow a systematic approach that involves three key steps. The first step is to establish the peptide backbone by creating a series of nitrogen-carbon-carbon (NCC) sets, which represent each amino acid. For a peptide with seven residues, we will draw seven NCC sets, resulting in a structure that looks like this: NCC, NCC, NCC, NCC, NCC, NCC, NCC. Each NCC set includes an alpha carbon, which is the central carbon atom in each amino acid. Thus, we identify the alpha carbons in our structure.

At the terminal ends of the peptide, we must include functional groups. The amino group at the N-terminus will be represented as NH₃⁺, while the carboxyl group at the C-terminus will be depicted as COO^-.

In the second step, we incorporate carbonyl groups (C=O) on the carbon atoms adjacent to the alpha carbons. This addition is crucial for representing the peptide bonds between amino acids. Furthermore, we must consider the chirality of the amino acids, noting that biological systems predominantly utilize L-amino acids. The configuration is determined by the orientation of the R group: if the R group points upwards, it is represented with a wedge, and if it points downwards, it is shown with a dash.

In the final step, we fill in the hydrogen atoms on the nitrogen atoms and add the specific R groups for each amino acid. The amino acids in this peptide are as follows:

• A for Alanine (Ala), which has a simple methyl group (–CH₃).
• I for Isoleucine (Ile), characterized by a branched structure derived from valine.
• M for Methionine (Met), which features a methyl thioether group, giving it a distinctive shape.
• H for Histidine (His), which includes a five-membered ring with two nitrogen atoms, resembling a horse.
• G for Glycine (Gly), the simplest amino acid with just a hydrogen atom as its R group.

Each amino acid's structure is carefully drawn, ensuring that the correct stereochemistry is maintained. For instance, the R group of histidine is depicted with two nitrogen atoms and double bonds, while glycine's minimalistic structure is represented by a single hydrogen. This comprehensive approach allows us to accurately depict the peptide structure, completing our drawing process.

To draw the peptide with the sequence pcynfqk, we will follow a systematic approach that involves three main steps. This peptide consists of seven amino acid residues, and we will begin by constructing the peptide backbone.

In the first step, we create the backbone by drawing a series of nitrogen-carbon-carbon (NCC) sets, which represent the connections between the amino acids. For this peptide, we will draw seven NCC sets, resulting in a linear structure. Each NCC set includes a nitrogen atom (N), an alpha carbon (C_α), and a carbonyl carbon (C). The alpha carbon is the central carbon in each NCC set, and it is crucial for determining the chirality of the amino acids.

At one end of the peptide, we will have a free amino group (NH₃⁺), and at the other end, a free carboxylate group (COO^-), which indicates the N-terminus and C-terminus of the peptide, respectively.

In the second step, we will add the carbonyl groups (C=O) to the backbone. These carbonyl groups are located on the carbon atoms adjacent to the alpha carbons. Additionally, we will consider the chirality of the amino acids, noting that biological systems predominantly utilize L-amino acids. To represent this, we will position the R groups accordingly: those pointing upwards will be drawn on wedges, while those pointing downwards will be on dashes.

In the final step, we will incorporate the side chains (R groups) of each amino acid. The amino acids represented in the sequence are:

• P - Proline: Its R group forms a cyclic structure connecting back to the nitrogen, resulting in a unique pentagonal shape.
• C - Cysteine: This amino acid features a sulfhydryl group (–SH) attached to an alanine backbone.
• Y - Tyrosine: Tyrosine is similar to phenylalanine but has a hydroxyl group (–OH) attached to the phenyl ring.
• N - Asparagine: This amino acid has an amide group (–C(=O)NH₂) attached to an alanine backbone.
• F - Phenylalanine: It consists of an alanine backbone with a phenyl group (a benzene ring) as its side chain.
• Q - Glutamine: Similar to asparagine, but with an additional methylene group (–CH₂) before the amide group.
• K - Lysine: This amino acid has a long aliphatic chain ending with an amino group (–NH₃⁺), giving it a positive charge.

By carefully drawing each amino acid's structure and ensuring the correct placement of hydrogens and functional groups, we successfully construct the complete peptide structure for pcynfqk. This exercise not only reinforces our understanding of peptide formation but also highlights the importance of amino acid properties in determining the overall structure and function of proteins.