Protein structure and folding
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- Protein structure and folding
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Protein structure and folding
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[post_date] => 2025-01-14 06:01:11
[post_date_gmt] => 2025-01-14 11:01:11
[post_content] => Practice Passage (Question 1-6)
*This passage is the property of Khan Academy and has been reformatted into an AAMC-style interface in their entirety by MedLife Mastery. MedLife Mastery does not endorse and is not an affiliate of Khan Academy.
A protein’s three dimensional shape comes from the arrangement of secondary structure elements such as α-helices and β-sheets that fold into identifiable conformations called motifs. Motifs are short segments of a protein’s structure, and the same arrangement can be found in many different proteins. For example, the β-turn links β-strands together and consists of four consecutive residues which allow the polypeptide chain to fold back on itself by nearly 180 degrees. The β-α-β motif consists of parallel β-strands that are connected by an α-helix. Secondary structure elements and motifs are arranged into compact independent 3D structures called domains. Levels of protein organization are shown in Figure 1.
Figure 1. Levels of protein organization The folding of protein domains is a spontaneous reaction when a negative change in Gibbs free energy (G) occurs, and the protein domain moves to a lower energy state. The driving force for protein folding is a result of both hydrophobic collapse and new bond formation (hydrogen bonds, electrostatic and van der Waals interactions) that lowers the free energy.
When amino acids form new bonds, heat energy is released; meanwhile, heat energy is absorbed to break these bonds with water. Therefore, the relative amount of bond formation to bond breakage in the unfolded and folded states will determine the change in enthalpy (ΔH). However, the basis of the hydrophobic effect (collapse) pertains more importantly to changes in a protein’s hydration shell. When a protein domain is present in its unfolded state, water molecules have to order themselves in ice-like structures around the hydrophobic groups of the polypeptide chain. When the protein domain collapses and places the hydrophobic side chains into the middle of the protein (Figure 2A), the hydration shells around the side chains are no longer required, and these water molecules become disordered.
Figure 2B shows the free energy of the native and denatured ensembles of a protein under conditions where the native state is favored. The free energy difference between these states (ΔG) is a measure of the stability of the protein. The transition state ensemble is a population of short-lived and partially folded conformations that cannot be directly observed in experiments but must be passed through to fold and defines the activation barrier for folding (ΔG# folding) and unfolding (ΔG# unfolding).
Figure 2. Energy changes associated with protein folding
Passage and figures adapted from Stollar EJ, Smith DP. Uncovering protein structure. Essays Biochem. 2020 Oct 8;64(4):649-680. doi: 10.1042/EBC20190042. Erratum in: Essays Biochem. 2021 Jul 26;65(2):407. PMID: 32975287; PMCID: PMC7545034.
[post_title] => Protein structure and folding
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[question] => Which of the following statements regarding protein structure are accurate?
I. The secondary structure of a protein is stabilized by hydrogen bonds between the C=O and NH groups of each peptide bond.
II. The overall 3D structure of a protein is mediated by interactions between amino acid side chains.
III. The primary structure of a protein is stabilized by stable hydrogen bonds.
IV. The tertiary structure of the protein is mediated by peptide bonds.
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[description] => Reason for the Correct Answer:
The primary structure of a protein consists of the sequence of amino acids.
These bonds form between the carboxyl group of one amino acid and the amino group of another, linking the amino acids together in a specific sequence. So, Statement III is incorrect.
Secondary structure refers to the local folded structures that form within a polypeptide due to interactions between atoms of the backbone (not the side chains). The most common types of secondary structures are alpha helices and beta sheets. These structures are stabilized by hydrogen bonds between the backbone atoms in different parts of the protein chain – specifically between the carbonyl oxygen of one amino acid and the hydrogen of the amide group of another amino acid. So, Statement I is correct.
https://commons.wikimedia.org/wiki/File:StrukturaSekondare.jpg
The tertiary structure of a protein refers to the overall three-dimensional folding of a single polypeptide chain. This structure is stabilized by various interactions and bonds between the side chains (R groups) of the amino acids in the protein. These include: hydrophobic interactions; hydrogen bonds, ionic bonds, and disulfide bridges between side chains; and Van der Waals interactions.
https://commons.wikimedia.org/wiki/File:Tertiary_protein_structure.png
Peptide bonds, which stabilize primary structure, are not involved in higher levels of protein organization like secondary, tertiary, or quaternary structure.
Accordingly, Statement II is correct, and Statement IV is incorrect.
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[answers] => Array
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[0] => Array
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[each_answer] => A.II only
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[1] => Array
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[each_answer] => B.I and II only
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[2] => Array
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[each_answer] => C.I and III only
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[3] => Array
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[each_answer] => D.II and IV only
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[1] => Array
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[quiz_unique_key] => 3873426850
[question] => The α-helix is a right-handed coiled secondary structure. Which of the following statements is NOT true regarding the α-helix structure?
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[answer] => 3
[description] => Reason for the Correct Answer:
The alpha helix is stabilized by interactions between backbone NH groups and C=O groups, 4 amino acids apart.
You should also be familiar with other features of the alpha helix, such as the fact that it completes a full turn a little less than the length of 4 amino acids (3.6 to be exact).
In an alpha helix, the amino acids are arranged in a right-handed coiled or spiral structure, resembling a spring. The R groups of the amino acids extend outward from the helix core.
https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/alpha-helix
The R groups do NOT face inwards, so C is the answer.
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[answers] => Array
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[0] => Array
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[each_answer] => A.A backbone NH group hydrogen bonds to the backbone C=O group of the amino acid located four residues earlier.
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[1] => Array
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[each_answer] => B.The polypeptide chain can twist in a regular coil shape, with the R-groups pointing outwards away from the peptide backbone.
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[each_answer] => C.The polypeptide chain can twist in a regular coil shape with the R-groups pointing inwards.
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[each_answer] => D.It takes less than 4 amino acid residues to complete a full turn of a helix.
)
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[2] => Array
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[quiz_unique_key] => 83407773
[question] => β-sheets are composed of two or more extended polypeptide chains called β-strands. The amino acid residues are arranged in a zigzag manner with the adjacent peptide bonds pointing in opposite directions. Which of the following is NOT true about β-sheets?
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[answer] => 1
[description] => Reason for the Correct Answer:
β-sheets can be formed by strands running in the same direction (parallel) or in opposite directions (antiparallel).
In β-sheets, the side chains of the amino acids project alternately above and below the plane of the sheet. This zigzag arrangement helps stabilize the β-sheet structure.
Alternating patterns can lead to amphipathic β-sheets, where one side is hydrophilic and the other side is hydrophobic. This property is important for the interaction of β-sheets with other molecules and within the protein’s overall structure.
In β-sheets, hydrogen bonds form between the NH group of one amino acid and the C=O group of another amino acid on an adjacent β-strand.
The hydrogen bonds typically occur between directly opposing residues (one position down on the adjacent strand) rather than three positions down. The pattern of hydrogen bonding does not skip several residues but is rather more immediate and direct between adjacent strands.
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[each_answer] => A.The NH group of each amino acid is bonded to the C=O group 3 positions down on the adjacent strand.
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[each_answer] => B.Sidechains from each of the residues point away from the sheets and alternate in opposite directions between residues.
)
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[each_answer] => C.It is common to see a pattern of alternating hydrophilic and hydrophobic residues in the primary structure, giving the β-sheets hydrophilic and hydrophobic faces.
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[each_answer] => D.They are arranged in either a parallel or antiparallel manner.
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[3] => Array
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[quiz_unique_key] => 2377279144
[question] => The most common β-turn-forming residues include which amino acids?
[value] => Array
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[answer] => 3
[description] => Reason for the Correct Answer:
β-turns are a type of secondary structure in proteins that allow the polypeptide chain to reverse its direction. They are often found connecting adjacent strands of antiparallel β-sheets.
β-turns typically involve four amino acid residues and are stabilized by a hydrogen bond between the C=O group of the first residue and the NH group of the fourth residue. Certain amino acids are more favorable for β-turn formation due to their structural properties.
Glycine is the smallest amino acid with only a hydrogen as its side chain, providing high flexibility and allowing it to fit into tight spaces within the turn.
Proline Proline has a unique cyclic structure that introduces a kink or bend in the polypeptide chain, making it ideal for the sharp turn required in a β-turn.
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[answers] => Array
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[0] => Array
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[each_answer] => A.Glycine, Tryptophan
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[each_answer] => B.Proline, Leucine
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[each_answer] => C.Glycine, Proline
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[each_answer] => D.Tyrosine, Proline
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[quiz_unique_key] => 2261298308
[question] => Which statement is true regarding the thermodynamics of protein folding?
[value] => Array
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[answer] => 3
[description] => Reason for the Correct Answer:
Protein folding is described as a spontaneous reaction that occurs when there is a negative change in Gibbs free energy (ΔG), as shown in Figure 2. As discussed in the passage, the driving force for protein folding includes both hydrophobic collapse and new bond formation, which contribute to lowering the free energy.
The passage states that when amino acids form new bonds during folding, heat energy is released (-ΔH), and when bonds with water are broken, heat energy is absorbed (+ΔH). The relative amount of bond formation versus bond breakage determines the change in enthalpy (ΔH).
So for the protein, there is a negative change in enthalpy, or a decrease in enthalpy.
As the passage states, the hydrophobic effect is crucial for folding. In the unfolded state, water molecules form ordered structures around hydrophobic groups. When the protein folds, these hydrophobic side chains are buried inside the protein, and the previously ordered water molecules become disordered.
This increases the entropy of the surrounding water molecules. This increase in entropy contributes to the overall favorability of protein folding.
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[answers] => Array
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[0] => Array
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[each_answer] => A.Protein folding results in an increase in enthalpy for the protein.
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[each_answer] => B.Protein folding results in an increase in entropy for the protein.
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[2] => Array
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[each_answer] => C.Protein folding results in an increase in entropy of the surrounding water molecules.
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[each_answer] => D.Protein folding results in an increase in Gibbs free energy of the surrounding water molecules.
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[quiz_unique_key] => 3892269748
[question] => The primary amino acid sequence of a protein is glycine-proline-X or glycine-X-hydroxyproline. X can be any of the other 17 amino acids, and every third amino acid is glycine. It is composed of 3 chains that are wound together to form a triple helix. It is abundantly found in the extracellular space of connective tissues. The protein and its categorization are:
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[answer] => 2
[description] => Reason for the Correct Answer:
The protein is composed of 3 chains that are wound together to form a triple helix. This structure is characteristic of certain types of proteins found in connective tissues.
Myosin is involved in muscle contraction and typically forms globular structures, not triple helices.
Insulin is involved in regulating blood sugar levels and does not match the structural characteristics described.
Keratin is a structural protein found in hair, nails, and skin; it is not a transport protein.
Collagen is a structural protein found in connective tissues like skin, tendons, and bones, where it provides rigidity and structural support. It has a primary sequence with glycine every third residue, often with proline and hydroxyproline and forms a triple helix structure composed of three chains.
https://simple.wikipedia.org/wiki/Collagen
)
[answers] => Array
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[0] => Array
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[each_answer] => A.myosin, a globular protein.
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[1] => Array
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[each_answer] => B.collagen, a structural protein.
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[each_answer] => C.insulin, a hormone.
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[each_answer] => D.keratin, a transport protein.
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