1.7 Proteins

1. AA water molecule is added between it and the end of the chain, joining the two together.
   A student who mixes up dehydration synthesis and hydrolysis picks this. Water is released when a peptide bond forms; water is added only when the bond is broken by hydrolysis.
2. BThe chain's last carboxyl group forms a covalent bond with the amino acid's amine group, releasing water. Correct
   A peptide bond, a covalent bond, forms between the carboxyl group at the end of the growing chain and the amine group of the new amino acid. The reaction is dehydration synthesis, so the equivalent of one water molecule is released.
3. CIts R group forms a covalent bond with the R group of the amino acid at the end of the chain.
   A student who thinks amino acids are joined through their R groups picks this. The chain is built by bonds between the carboxyl and amine groups that every amino acid has; R groups project from the chain.
4. DIts amine group is held to the carboxyl group at the end of the chain by a hydrogen bond.
   A student who thinks peptide bonds are hydrogen bonds picks this. The amine and carboxyl groups are joined by a covalent bond; hydrogen bonds are weaker attractions that help fold the chain.

CED 1.7.A.1 · Read this in Fix

1. AThey are the same in every amino acid, which differ instead in their amine and carboxyl groups.
   A student who thinks amino acids differ in their amine and carboxyl groups picks this. Every amino acid has the same amine and carboxyl groups; only the R group varies.
2. BThey form the covalent bonds that join each amino acid to the next one in the chain.
   A student who thinks amino acids are joined through their R groups picks this. Each amino acid is joined to the next by a peptide bond between its carboxyl group and the next amino acid's amine group.
3. CThey are nitrogenous bases that pair with one another to hold the chain in its shape.
   A student who confuses amino acids with nucleotides picks this. Nitrogenous bases are parts of nucleotides in DNA and RNA; amino acids have R groups, which are not bases.
4. DThey differ among amino acids, and their chemical properties affect how the chain folds. Correct
   The R group is the only part that differs among amino acids. Whether it is nonpolar, polar or ionic determines which interactions it forms, and so how that region of the protein folds.

CED 1.7.A.2 · Read this in Fix

1. AThe same shape, because a chain's shape depends on which amino acids it contains and not on their order
   A student who thinks shape depends only on which amino acids are present picks this. Rearranging the amino acids moves R groups to new positions, which changes which interactions can form as the chain folds.
2. BDifferent shapes, because the order of the R groups determines which interactions form during folding Correct
   P and Q have different sequences, so they have different primary structures. The sequence determines where each R group sits along the chain and so which interactions form during folding; different orders are therefore likely to give different shapes.
3. CThe same shape, because two chains made of the same amino acids have the same primary structure
   A student who thinks primary structure means which amino acids are present picks this. Primary structure is the order of the amino acids, so P and Q have different primary structures.
4. DDifferent shapes, because each chain folds at random whatever the sequence of its amino acids
   A student who thinks polypeptides fold at random picks this. Folding is not random: the sequence determines the shape, so identical chains fold alike and P and Q differ because their sequences differ.

CED 1.7.A.3 · Read this in Fix

1. AInteractions between the R groups that stick out from the two strands
   A student who thinks secondary structure is held by R-group interactions picks this. The model shows the R groups pointing away from the dashed lines; the dashed lines join the backbones.
2. BPeptide bonds between amino acids lying across from each other on the strands
   A student who thinks the bonds between amine and carboxyl groups are hydrogen bonds picks this, calling the backbone-to-backbone links peptide bonds. Peptide bonds join neighboring amino acids along each strand; the dashed lines are weaker hydrogen bonds between the strands.
3. CHydrogen bonds between atoms of the backbones of the two strands Correct
   In the model, every dashed line joins the backbone of one strand to the backbone of the other, and no dashed line touches an R group. Secondary structures such as beta-pleated sheets are held by hydrogen bonds between backbone atoms.
4. DCovalent bonds between backbone atoms, which make the sheet's shape fixed
   A student who thinks hydrogen bonds are covalent bonds picks this. The links between the strands are hydrogen bonds, which are much weaker than covalent bonds and do not share electrons between the strands.

CED 1.7.A.4 · Read this in Fix

1. AThey form between R groups of amino acids that are next to each other in the chain.
   A student who thinks folding interactions form only between neighbors picks this. None of the interacting pairs in the model are neighbors; the closest pair, 3 and 8, is five positions apart.
2. BThey form between R groups of amino acids that are far apart in the sequence. Correct
   The model shows R groups of amino acids 2 and 9, 3 and 8, and 7 and 14 interacting. These pairs are 5 to 7 positions apart along the chain; folding brings them close together in space.
3. CThey are all covalent bonds, like the bonds that join amino acids into a chain.
   A student who thinks tertiary structure is held by covalent bonds picks this. Only the disulfide bridge between 2 and 9 is covalent; the model also shows a hydrogen bond and an ionic interaction.
4. DThey form at random between any R groups that happen to meet as the chain folds.
   A student who thinks polypeptides fold at random picks this. Which interactions form is determined by the amino acid sequence, so every copy of this polypeptide folds the same way.

CED 1.7.A.5 · Read this in Fix

1. AIts polypeptides are no longer joined end to end by the peptide bonds that link them into one chain.
   A student who thinks the polypeptides of a multi-polypeptide protein are joined by peptide bonds picks this. Each polypeptide is a separate chain; they are held together by interactions such as hydrogen bonds and ionic and hydrophobic interactions.
2. BIts function depends on the quaternary structure formed by interactions between the polypeptides. Correct
   Quaternary structure arises from interactions between multiple polypeptides, and all levels of structure determine function. The replaced amino acid prevents the polypeptides from associating, so the functional four-polypeptide shape does not form.
3. CIts amino acid sequence has changed, and a protein's function depends on its sequence, not its shape.
   A student who thinks function depends on sequence alone picks this. The sequence did change, but it affects function by changing shape: here the change prevents the polypeptides from associating into the functional structure.
4. DAny change in the amino acid sequence of a protein destroys its function, wherever it occurs.
   A student who thinks every change in sequence destroys function picks this. Many replacements have little or no effect; this one matters because it prevents the polypeptides from associating.

CED 1.7.A.6 · Read this in Fix

1. ABond W Correct
   Bond W is a covalent bond joining the backbones of amino acids 2 and 3, which are next to each other in the chain. A peptide bond joins the carboxyl group of one amino acid to the amine group of the next, so it links neighboring backbones.
2. BBond X
   A student who thinks amino acids are joined through their R groups picks this. Bond X is covalent, but it joins the R groups of amino acids 2 and 7, which are far apart in the chain; it helps fold the chain rather than build it.
3. CBond Y
   A student who thinks amino acids are held together by ionic attractions picks this. Bond Y is an ionic attraction between the charged R groups of amino acids 3 and 6; it is not a covalent bond and does not join neighbors.
4. DBond Z
   A student who thinks peptide bonds are hydrogen bonds picks this. Bond Z is a hydrogen bond between the backbones of amino acids 1 and 8; it helps fold the chain, but the amino acids are joined by covalent peptide bonds.

CED 1.7.A.1 · Read this in Fix

1. A75%
   A student who gives the new value as a percentage of the original picks this: 48/64 × 100 = 75%. That is the percentage of the original activity that remains, not the percent decrease.
2. B16%
   A student who reports the difference between the values as the percent change picks this. The difference, 16 μmol/min, must be divided by the original value, 64 μmol/min, to give a percentage.
3. C25% Correct
   The activity fell from 64 to 48 μmol/min, a change of 16 μmol/min. Percent decrease = 16/64 × 100 = 25%.
4. D33%
   A student who divides the change by the new value picks this: 16/48 × 100 = 33%. Percent change is calculated relative to the original value, 64 μmol/min.

Working From the table: original enzyme (nonpolar R group at position 72) 64 μmol/min; Variant 2 (polar R group) 48 μmol/min. Percent change = (new − original)/original × 100 = (48 − 64)/64 × 100 = −25%, a 25% decrease. Distractors: new as a percentage of the original, 48/64 × 100 = 75%; the difference reported as a percentage, 64 − 48 = 16 → 16%; the change divided by the new value, 16/48 × 100 = 33%.

CED 1.7.A.2 · Read this in Fix

1. AThe protein will keep its shape and function, as one amino acid is too small a part of the chain to matter.
   A student who thinks a single amino acid is too small a change to matter picks this. Position 40 is in the interior, where R-group interactions hold the shape, so replacing a nonpolar R group with an ionic one can change the folding.
2. BThe protein will lose all of its function, as any change in an amino acid sequence destroys function.
   A student who thinks every change in sequence destroys function picks this. The replacement can change the folding, but whether and how much function is lost depends on the change; total loss is not the only possible outcome.
3. CThe new ionic R group may pack more tightly among the nonpolar R groups, stabilizing the interior.
   A student who thinks charged R groups belong in a protein's interior picks this. Ionic R groups interact with water and with oppositely charged groups, not with nonpolar R groups, so placing one among nonpolar R groups tends to disrupt the interior.
4. DThe region near the new amino acid may fold differently, altering the protein's shape and function. Correct
   The nonpolar R group at position 40 interacts with the nonpolar R groups around it. A charged R group cannot take part in these hydrophobic interactions and interacts with water instead, so that region may fold differently, changing the shape and possibly the function.

CED 1.7.A.2 · Read this in Fix

1. ATube 1, which differs from tube 2 only in having the original protein Correct
   The claim is about the effect of the change at position 118. Tube 1 is identical to tube 2 except that it contains the original protein, so any difference in hormone bound can be attributed to the replaced amino acid.
2. BTube 3, which contains no protein, so nothing at all can bind the hormone
   A student who thinks the best control is one with nothing added picks this. Tube 3 shows how much hormone is measured without any protein, but it cannot show whether the variant binds differently from the original protein.
3. CTube 4, which contains the same variant protein as tube 2 does
   A student who thinks the control should receive the same treatment as the experimental tube picks this. Tube 4 has the same variant protein and lacks the hormone, so it cannot show the effect of the change at position 118.
4. DNo other tube, as tube 2's result on its own will show any change
   A student who thinks one result is enough to test a claim picks this. Without the original protein under the same conditions, there is nothing to compare the variant's binding with.

CED 1.7.A.3 · Read this in Fix

1. AA helix is held by bonds between R groups, and every kind of R group can form those bonds equally well.
   A student who thinks secondary structure is held by R-group interactions picks this. Helices are held by hydrogen bonds between backbone atoms; R groups differ in their properties, so they do not all form the same bonds.
2. BA helix forms wherever the folding chain happens to coil at random, whatever the sequence.
   A student who thinks polypeptides fold at random picks this. Folding is determined by the sequence; helices form because hydrogen bonds between backbone atoms stabilize that local shape.
3. CA helix is formed by the peptide bonds, which join neighboring amino acids together in every chain.
   A student who thinks peptide bonds are hydrogen bonds picks this. Peptide bonds join neighboring amino acids into the chain; the helix is held by hydrogen bonds between backbone atoms of amino acids a few positions apart.
4. DA helix is held by hydrogen bonds between backbone atoms, which are present whatever the R groups are. Correct
   An alpha-helix is a secondary structure: it is held by hydrogen bonds between atoms of the polypeptide backbone. The backbone is built from the groups that all amino acids share, so helices can form in many different sequences.

CED 1.7.A.4 · Read this in Fix

1. AThe polypeptide breaks into separate fragments at the amino acids whose R groups had been linked together.
   A student who thinks loss of structure means the chain breaks picks this. The chain is held together by peptide bonds, which the chemical does not break, so the polypeptide stays in one piece.
2. BIts alpha-helices may unwind, because disulfide bridges hold the coils of each helix in their shape.
   A student who thinks secondary structure is held by interactions between R groups picks this. Alpha-helices are held by hydrogen bonds between backbone atoms, which the chemical does not affect.
3. CIts amino acid sequence stays the same, but its overall shape may change as some R groups are no longer linked. Correct
   Peptide bonds are not broken, so the primary structure is unchanged. Disulfide bridges are covalent links between R groups that help hold the tertiary structure, so breaking them may let parts of the chain move apart, changing the shape.
4. DIt unfolds completely, because disulfide bridges are the main bonds holding its tertiary structure.
   A student who thinks tertiary structure is held mainly by covalent bonds picks this. Hydrogen bonds, hydrophobic interactions and ionic interactions also hold the tertiary structure and are not affected, so complete unfolding is not expected.

CED 1.7.A.5 · Read this in Fix

1. AActivity was high with α and β together but low with either of the two alone. Correct
   The mixture had a mean activity of 88 μmol/min, while α alone (3) and β alone (6) had very little; the error bars for the mixture do not overlap with either single polypeptide.
2. BThe mixture's activity was roughly the sum of the activities of α and β alone.
   A student who thinks each polypeptide contributes its share of the activity picks this. The sum of α alone and β alone is about 9 μmol/min, far below the mixture's 88 μmol/min.
3. CPolypeptides α and β alone were each about as active as the two mixed together.
   A student who thinks a polypeptide with the correct sequence is active on its own picks this. The graph shows each polypeptide alone with very low activity compared with the mixture.
4. DPolypeptide β alone was significantly more active than polypeptide α alone.
   A student who treats any difference between means as real picks this. The mean for β alone (6) is higher than for α alone (3), but their ±2 SE error bars overlap, so the difference has not been shown to be significant.

CED 1.7.A.6 · Read this in Fix