The correct answer is B. Zwitterions. Explanation 1: A zwitterion is a molecule that contains an equal number of positively and negatively charged functional groups. In the case of amino acids, this means they have a positively charged amino group (-NH3+) and a negatively charged carboxyl group (-COO-). In a neutral solution (pH around 7), the amino group is protonated (gains an H+) and the carboxyl group is deprotonated (loses an H+). This results in the formation of a zwitterion, where the molecule has a net charge of zero but still possesses internal charges. The other options are incorrect because: * A. Positively charged compounds: This would occur at a very acidic pH, where both groups would be protonated. * C. Negatively charged compounds: This would occur at a very basic pH, where both groups would be deprotonated. * D. Hydrophobic molecules: While some amino acids have hydrophobic side chains, the central structure of an amino acid in a neutral solution is a zwitterion, which is water-soluble due to its charges. In summary, the zwitterionic nature of amino acids in neutral solutions is a fundamental property that influences their behavior and function in biological systems.

The correct answer is B. -1. Explanation 2: Glutamic acid is an acidic amino acid, meaning it has an additional carboxyl group in its side chain, in addition to the carboxyl and amino groups present in all amino acids. At pH 7 (physiological or neutral pH): 1. The alpha carboxyl group (on the alpha carbon, common to all amino acids) will be deprotonated (-COO-), contributing a negative charge. 2. The amino group (also on the alpha carbon) will be protonated (-NH3+), contributing a positive charge. 3. The side chain carboxyl group (which makes glutamic acid an acidic amino acid) will also be deprotonated (-COO-), contributing another negative charge. Therefore, the net charge on the glutamic acid molecule at pH 7 will be: -1 (alpha carboxyl) +1 (amino) -1 (side chain carboxyl) = -1 The other options are incorrect because: * A. -2: This would occur at a very basic pH, where all groups would be deprotonated. * C. 0: This would occur at the isoelectric point of glutamic acid, which is around pH 3.22. At this point, the net charge on the molecule is zero, but there are positive and negative charges that cancel each other out. * D. +1: This would occur at a very acidic pH, where all groups would be protonated. In summary, the negative charge of glutamic acid at physiological pH is crucial for its function in biological systems, such as in neurotransmission and metabolism.

The correct answer is C. They are hydrophobic and are found buried within proteins. Explanation 3: * Hydrophobic: Nonpolar R groups are primarily composed of hydrocarbon chains or aromatic rings. These structures do not interact favorably with water, which is a polar solvent. Therefore, these R groups are hydrophobic ("water-repelling"). * Buried within proteins: In an aqueous environment, such as the inside of a cell, proteins tend to fold in a way that the hydrophobic R groups cluster inside the protein structure, away from contact with water. This increases the stability of the protein by minimizing unfavorable interactions between nonpolar R groups and water. The other options are incorrect because: * A. They are hydrophilic and are found buried within proteins. Hydrophilic ("water-loving") R groups interact favorably with water and tend to be exposed on the surface of proteins. * B. They are hydrophilic and are found on the surfaces of proteins. This statement is true for polar or charged R groups, but not for nonpolar R groups. * D. They are hydrophobic and are found on the surfaces of proteins. This arrangement would be energetically unfavorable, as it would expose the hydrophobic R groups to water. In summary, the tendency of nonpolar R groups to cluster inside proteins is a fundamental principle in the folding and stability of proteins in aqueous solution.

The correct answer is A. Primary structure. Explanation 4: * Primary structure: The primary structure of a protein is simply the linear sequence of amino acids that make it up. A cDNA (complementary DNA) contains the genetic information necessary to synthesize a protein, so from the cDNA sequence, the amino acid sequence, and thus the primary structure of the protein, can be directly deduced. * Secondary structure: Secondary structure refers to local folding patterns of the polypeptide chain, such as alpha helices and beta sheets. While there are computer programs that can predict secondary structure with some accuracy based on the amino acid sequence, these predictions are not always perfect and can be affected by factors such as long-range interactions within the protein. * Tertiary structure: Tertiary structure describes the overall three-dimensional arrangement of all the atoms in the protein. Predicting tertiary structure from the amino acid sequence is a much more complex problem, and while there have been significant advances in recent years (such as with AlphaFold), it remains a major challenge in bioinformatics. * Quaternary structure: Quaternary structure refers to the association of multiple polypeptide chains (subunits) to form a complete functional protein. Predicting quaternary structure is even more difficult than predicting tertiary structure, as it requires knowing not only the structure of each individual subunit but also how they interact with each other. In summary, the primary structure is the only level of protein structure that can be directly and accurately determined from the cDNA sequence. The prediction of higher levels of structure, while possible in some cases, remains an active area of research and presents significant challenges.

The correct answer is C. 6. Explanation 5: A tripeptide is formed by three amino acids joined by peptide bonds. In this case, we have three different amino acids (valine, alanine, and leucine) to form the tripeptide. To calculate the number of different possible tripeptides, we need to consider the different ways these amino acids can be arranged. * For the first position in the tripeptide, we have 3 choices (any of the three amino acids). * Once the first amino acid has been chosen, there are 2 choices left for the second position. * Finally, there is only 1 choice left for the third position. Therefore, the total number of different possible tripeptides is 3 * 2 * 1 = 6 The other options are incorrect because: * A. 1: This would imply that there is only one possible combination of the three amino acids, which is incorrect. * B. 3: This could result from considering only the three possible options for the first position, ignoring the remaining permutations. * D. 27: This number would be obtained if each position in the tripeptide could be occupied by any of the three amino acids, which would give us 3 * 3 * 3 = 27 combinations. However, since we only have one molecule of each amino acid, each can only be used once in the tripeptide. In summary, the number of different tripeptides that can be formed from three different amino acids is equal to the factorial of the number of amino acids (3! = 3 * 2 * 1 = 6).

The correct answer is B. The entropy of the water increases; the entropy of the protein decreases. Explanation 6: * Protein entropy: When a protein folds, it goes from an unfolded state with many possible conformations (high disorder, high entropy) to a folded state with a specific and much more ordered conformation (low disorder, low entropy). Therefore, the entropy of the protein decreases during folding. * Water entropy: In the unfolded state, the hydrophobic residues of the protein are exposed to water, forcing water molecules to form ordered (cage-like) structures around these residues to minimize unfavorable interactions. When the protein folds, the hydrophobic residues become buried inside the structure, releasing the water molecules from these ordered structures. This increases the disorder and, therefore, the entropy of the water. * Entropic balance: Although the decrease in protein entropy is thermodynamically unfavorable, the increase in water entropy partially compensates for this effect. Protein folding is made possible by other favorable factors, such as the formation of hydrogen bonds, electrostatic interactions, and the hydrophobic effect, which contribute to lowering the total free energy of the system. The other options are incorrect because: * A. The entropy of both the water and the protein increases. The entropy of the protein decreases during folding. * C. The entropy of the water decreases; the entropy of the protein increases. The entropy of the water increases and the entropy of the protein decreases. * D. The entropy of both the water and the protein decreases. The entropy of the water increases during folding. In summary, the change in entropy during protein folding is a balance between the decrease in conformational entropy of the protein and the increase in water entropy due to the release of ordered water molecules.

The correct answer is C. Hydrogen bonds. Explanation 7: The alpha helix is a type of secondary structure in proteins, characterized by a regular helical coil of the polypeptide chain. The stability of this structure is primarily due to the formation of hydrogen bonds between the carbonyl group (C=O) of one amino acid and the amino group (N-H) of another amino acid located four residues further along the sequence. These hydrogen bonds are established along the axis of the helix, contributing to its cohesion and rigidity. The other options are less likely or incorrect: * A. Disulfide bonds: Disulfide bonds are strong covalent bonds formed between two cysteine residues. While they can contribute to the stability of some proteins, they are not the primary stabilizing force of the alpha helix. * B. Hydrophobic effects: Hydrophobic effects play an important role in the overall folding of proteins, but they are not the main force that holds the alpha helix together. * D. Ionic attractions between side chains: Ionic attractions can occur between charged side chains of amino acids, but their contribution to the stability of the alpha helix is generally less than that of hydrogen bonds. In summary, hydrogen bonds are the main force that stabilizes the structure of the alpha helix in proteins.

The correct answer is C. Moving it to a more hypotonic environment. Explanation 8: Protein denaturation involves the loss of its native three-dimensional structure, leading to the loss of its biological function. Several factors can cause denaturation, including: * A. Heating the protein to 100°C: Heat increases the kinetic energy of molecules, which can break the weak bonds (such as hydrogen bonds) that maintain the protein's structure. * B. Adding 8 M urea: Urea is a chaotropic agent that disrupts non-covalent interactions in proteins, destabilizing their structure. * D. Adding a detergent such as sodium dodecyl sulfate (SDS): Detergents are amphiphilic molecules that can interact with both hydrophobic and hydrophilic parts of proteins, disrupting their native structure. C. Moving it to a more hypotonic environment: A hypotonic environment has a lower concentration of solutes compared to the inside of the cell or the protein. This would cause water to move into the cell or protein, which could lead to swelling or even rupture (lysis), but it is less likely to cause direct protein denaturation compared to the other factors mentioned. In summary, moving a protein to a more hypotonic environment is less likely to cause its denaturation compared to heat, urea, or detergents, which directly act on the bonds and interactions that maintain the protein's structure.

The correct answer is C. Phenylalanine. Explanation 9: The cell membrane is primarily composed of a lipid bilayer, which is a hydrophobic (nonpolar) environment. For an alpha helix to cross this membrane, the amino acids that make up the transmembrane region must also be hydrophobic, so they can interact favorably with the interior of the bilayer. * Phenylalanine: It is a nonpolar amino acid with an aromatic ring in its side chain. This feature makes it hydrophobic and, therefore, ideal for being part of the transmembrane portion of an alpha helix. The other options are incorrect because: * Glutamate and Aspartate: They are acidic amino acids with a negative charge at physiological pH. Their charged side chains are hydrophilic and would not interact favorably with the hydrophobic interior of the membrane. * Lysine: It is a basic amino acid with a positive charge at physiological pH. Like acidic amino acids, its charged side chain is hydrophilic and would not be suitable for the transmembrane region. In summary, hydrophobic amino acids, such as phenylalanine, are most likely to be found in the transmembrane portion of an alpha helix, as their nonpolar nature allows them to interact favorably with the hydrophobic environment of the lipid bilayer.

The correct answer is D. Serine, threonine, and isoleucine. Explanation 10: A chiral carbon is a carbon atom that is attached to four different groups. This gives it the property of having two distinct spatial configurations, called enantiomers, which are non-superimposable mirror images of each other. * Threonine: It has a hydroxyl group (-OH) in its side chain, attached to a carbon that is also bonded to a hydrogen, a methyl group, and the rest of the amino acid molecule. This makes this carbon chiral. * Isoleucine: It has a branched side chain, with a carbon attached to a hydrogen, a methyl group, an ethyl group, and the rest of the amino acid molecule. This carbon is also chiral. * Serine: Although it has a hydroxyl group in its side chain, it is attached to a carbon that is also bonded to two hydrogens, which does not meet the condition of having four different groups. Therefore, serine does not have a chiral carbon in its side chain. In summary, only threonine and isoleucine have a chiral carbon in their side chain, which allows them to exist in two distinct enantiomeric forms.

The correct answer is B. Tertiary to quaternary. Explanation 11: * Tertiary structure: It refers to the overall three-dimensional arrangement of a single polypeptide chain, including all its secondary structure elements (alpha helices, beta sheets, etc.) and the interactions between them. In the inactive state, receptor tyrosine kinases exist as monomers, each with its own defined tertiary structure. * Quaternary structure: It refers to the association of multiple polypeptide chains (subunits) to form a complete functional protein. In this case, the dimerization of receptor tyrosine kinases upon ligand binding involves the formation of a quaternary structure, where two monomers (each with its own tertiary structure) associate to form an active dimer. * Other levels of structure: * Primary structure: It is the linear sequence of amino acids of a protein. It does not change during dimerization. * Secondary structure: These are the local folding patterns of the polypeptide chain (alpha helices, beta sheets). While there may be subtle changes in secondary structure during dimerization, the main change is at the higher level of organization, going from individual monomers (tertiary structure) to an active dimer complex (quaternary structure). Therefore, the largest change in protein structure during the activation of receptor tyrosine kinases is from tertiary (individual monomers) to quaternary (active dimer).

The correct answer is A. Histidine. Explanation 12: Histidine has a side chain containing an imidazole group, which can ionize at physiological pH (around 7). This means it can accept or donate a proton, acquiring either a positive or neutral charge, respectively. This ionization capability gives histidine an important role in many biological processes, such as enzymatic catalysis and pH regulation. The other options are incorrect because: * Leucine: It has an aliphatic hydrophobic side chain, which cannot ionize. * Proline: Its side chain forms a cyclic structure with the amino group of the alpha carbon, limiting its ionization capability. * Threonine: It has a hydroxyl group in its side chain, which can form hydrogen bonds but does not ionize at physiological pH. In summary, histidine is the only amino acid among the given options that has a side chain capable of ionizing in cells, which gives it unique chemical and functional properties.

The correct answer is D. 9.8. Explanation 13: The correct answer is D. 9.8 because the isoelectric point is calculated by averaging the two pKa values that surround the zwitterionic form: pI = (9 + 10.5) / 2 = 9.75 This value is closest to 9.8.

The correct answer is D. To direct them to an organelle, the cell membrane, and add a cofactor necessary for their activity. Explanation 14: Protein conjugation is a process in which a chemical group or molecule is added to a protein. This can serve several purposes, including: 1. Targeting: * Organelles: Proteins can be conjugated with specific signal sequences that direct them to different organelles within the cell, such as the nucleus, endoplasmic reticulum, or mitochondria. * Cell membrane: Some proteins need to be anchored to the cell membrane to fulfill their function. Conjugation with lipids or glycolipids can facilitate this insertion into the membrane. 2. Activity: * Cofactors: Many proteins require cofactors (non-protein molecules) to be active. Conjugation can be a way to covalently or non-covalently attach these cofactors to the protein. The other options are incorrect because they are too limited: * A. Only to direct them to a particular organelle. Conjugation can also direct proteins to the cell membrane and add cofactors. * B. Only to direct them to the cell membrane. Conjugation can also direct proteins to organelles and add cofactors. * C. To direct them to the cell membrane and add a cofactor necessary for their activity. Conjugation can also direct proteins to organelles. In summary, protein conjugation is a versatile process that can serve multiple purposes, including targeting different destinations within the cell and adding cofactors necessary for their activity.

The correct answer is B. Glycine. Explanation 15: Collagen is a key structural protein in connective tissue, characterized by its triple helix structure. This unique structure requires specific amino acids to maintain its stability and function. * Glycine: Glycine is the smallest and simplest amino acid, with a hydrogen atom as its side chain. Its small size allows the three collagen chains to coil tightly together, forming the compact triple helix. In fact, approximately every third amino acid in collagen is glycine. The other options are less likely or incorrect: * Proline: While proline is important for the formation of collagen's helical structure, its cyclic side chain introduces rigidity into the polypeptide chain, limiting its presence compared to glycine. * Threonine and Cysteine: These amino acids have larger side chains that can interfere with the tight packing required for the collagen triple helix. Therefore, they are found in lower concentrations in collagen compared to glycine. In summary, glycine is the most abundant amino acid in collagen due to its small size, which is essential for the formation and stability of the characteristic triple helix of this protein.