Unit 1 · Topic 1.7 end-of-topic test
Suggested time: about 47 minutes. Answer everything, then press Submit the test to see the feedback and scoring guides.
The figure shows two different amino acids drawn side by side. The parts of each are numbered 1 to 4.
Which number marks the amine group?
Three R groups, cut from three different amino acids, are drawn below, numbered 1 to 3.
Which classification gives the three R groups in the order 1, 2, 3?
An R group ends in an O–H bond. A student says the R group must be charged, because its oxygen is δ− and its hydrogen is δ+.
Which description of this R group is correct?
The figure shows two amino acids that have just been joined. Two of the bonds are labeled b and c.
Which labeled bond is the peptide bond, and what left the two amino acids as it formed?
A cell builds a polypeptide from twelve amino acids, adding them one after another.
How many peptide bonds does the finished chain contain, and how are its amino acids arranged?
Two polypeptides are each built from the same twenty amino acids, one of each kind, but joined in a different order.
What should you predict about the two proteins they become?
A protein chain is held in its folded shape by bonds and attractions of several kinds. Some of them involve only the repeating backbone of the chain; others involve the R groups.
Which level of protein folding is held together by bonds along the backbone alone, with no part played by R groups?
The figure shows a stretch of one polypeptide drawn as a line that turns back on itself, so two lengths of the chain lie side by side. The short lines marked R are its R groups. Dashed lines run between the two lengths of chain.
Which level of structure is shown, and what are the dashed lines?
Two hydrogen bonds are found inside the same folded protein. Hydrogen bond X joins two atoms of the polypeptide backbone a few amino acids apart. Hydrogen bond Y joins two polar R groups on stretches of the chain that are far apart in the sequence.
Which level of structure does each hydrogen bond belong to?
The figure shows two R groups on distant parts of one folded polypeptide, drawn close together. One carries a full positive charge and the other a full negative charge.
Which interaction is drawn, and which level of structure does it help hold?
A hairdresser gives straight hair a curl that lasts for months. The first solution breaks the disulfide bridges in the hair’s keratin chains. The hairdresser winds the hair into curls, then applies the second solution.
Why does the hair keep its new curl?
A protein floats in the watery inside of a cell. One stretch of its chain is buried in the middle of the folded molecule, well away from the water.
What is most likely true of the R groups along that buried stretch?
Two proteins are compared. Protein A is one folded chain of 240 amino acids. Protein B is three folded chains of 80 amino acids each, held tightly against one another.
Which levels of structure does each protein have?
Hemoglobin's four folded chains fit together to make pockets that each hold one oxygen molecule. A biologist examining a sample of hemoglobin sees that some of the chains have folded into a different shape, with no pockets. Every one of those chains still has its full amino-acid sequence.
Would that hemoglobin carry oxygen, and why?
Raw fish flesh is translucent and soft. After cooking it is opaque and firm, and it does not become translucent again as it cools. Nobody added anything to it; heating was the only change.
What has happened to the protein molecules in the fish?
A protein is heated until it loses its shape and stops working.
Which feature of the protein is the same before and after the heating?
A protein gives off green light, and its brightness can be measured. Researchers made two variants, each with one amino acid replaced, and measured all three under the same conditions. Original protein: 100 units. Variant P, a nonpolar R group replaced by a different nonpolar R group: 96 units. Variant Q, a negatively charged R group replaced by a positively charged R group: 18 units.
Which best explains why the two substitutions had such different effects?
A protein floats in the watery inside of a cell. Deep in its interior, a stretch of nonpolar R groups is clustered together. In a variant of this protein, one of those interior amino acids is replaced by an amino acid with a charged R group. The chain is the same length and every other amino acid is unchanged.
What is the most likely effect of this substitution?
(a) Describe the primary structure of one hemoglobin chain, including the kind of bond that holds its amino acids together. (1 point)
A full-credit answer: The primary structure of one chain is the specific order of its amino acids from first to last, held together by peptide bonds: the covalent bond between the carboxyl group of one amino acid and the amine group of the next.
Check the box for each point your answer earns
Accept: the peptide bond described as the covalent bond between the carboxyl group of one amino acid and the amine group of the next, or as the bond formed by dehydration synthesis.
Do not award for describing the fold or shape of the chain, or for 'the amino acids it contains' without their order.
Common slip: Describing the fold, or listing which amino acids are present. Primary structure is their order, held by peptide bonds.
(b) Explain how the order of amino acids in a chain determines the three-dimensional shape the chain folds into. (1 point)
A full-credit answer: The order of amino acids sets the order of R groups along the chain, and the R groups fold it: nonpolar R groups gather together away from water, polar and charged R groups face the water, and R groups on distant parts of the chain hold one another by hydrogen bonds, ionic interactions or disulfide bridges.
A different order gives a different set of interactions and a different fold.
Check the box for each point your answer earns
Accept: an answer naming at least one specific R-group interaction (hydrophobic interaction, hydrogen bond, ionic interaction, disulfide bridge, or attraction to water) and linking it to the fold.
Do not award for 'the sequence determines the shape' restated without any mechanism.
Common slip: Writing ‘the sequence determines the shape’ and stopping. Name at least one R-group interaction and say how it folds the chain.
(c) Make a claim about how this substitution would most likely affect hemoglobin molecules in the watery inside of a red blood cell. (1 point)
A full-credit answer: The variant hemoglobin molecules stick to one another into fibers, so they carry oxygen less well.
Check the box for each point your answer earns
Accept: 'the molecules stick together', 'the nonpolar patches on neighboring molecules gather together away from water', or 'the shape changes so the pockets that hold oxygen are affected'.
Do not award: 'nothing changes because only one amino acid differs', or a claim that the chain breaks or unfolds completely.
Common slip: Claiming no change because only one amino acid differs. One surface R group that water excludes is enough to change how the molecules behave.
(d) Support your claim using the relationship between a protein's shape and its function. (1 point)
A full-credit answer: A protein’s function depends on its shape.
The shape depends on how its R groups interact with water and with one another.
In the variant, a surface R group has changed from charged to nonpolar, so water is no longer attracted to that spot.
So the nonpolar patches on neighboring molecules settle against one another, and the molecules stick together.
The stuck-together molecules no longer hold their working shape, so they carry oxygen less well.
Check the box for each point your answer earns
Accept: a response that explicitly links the R-group change to a shape change and the shape change to a change in function.
Do not award: the claim restated without connecting shape to function.
Common slip: Repeating the prediction. The justification must connect the R-group change to the shape and the shape to the job.
(a) Describe the level of structure shown at W, and the level of structure shown by chain 1 and chain 2 fitting together. (1 point)
A full-credit answer: W is secondary structure, an alpha helix held by hydrogen bonds between backbone atoms of one turn and the next; chain 1 and chain 2 fitting together is quaternary structure, two separately folded polypeptides making one protein.
Check the box for each point your answer earns
Accept: 'alpha helix' or 'a coil held by backbone hydrogen bonds' for W.
Do not award if W is called tertiary structure, or if the contact between the two chains is called tertiary structure.
Common slip: Calling W or the fit between the two chains tertiary structure. Tertiary structure is the fold of one chain; a coil held by backbone hydrogen bonds is secondary, and two chains fitting together is quaternary.
(b) Describe one of the hydrogen bonds at W: name the two backbone groups involved, state the partial charge on each, and say which atom of one group attracts which atom of the other. (1 point)
A full-credit answer: One hydrogen bond at W joins a backbone C=O group on one turn of the coil to a backbone N–H group on the next turn.
The O of the C=O group is δ−.
The H of the N–H group is δ+.
So the δ+ H of the N–H group attracts the δ− O of the C=O group; that attraction is the hydrogen bond.
Check the box for each point your answer earns
Accept: the two groups named and the H-to-O attraction stated without the δ+ and δ− labels.
Do not award: a hydrogen bond between two R groups, the partial charges reversed, or the N named as the atom that attracts the O.
Common slip: Placing the hydrogen bond between two R groups, or naming the N as the atom that attracts the O. The bonds at W join backbone groups, and it is the δ+ H of the N–H that is attracted to the δ− O of the C=O.
(c) Explain why the nonpolar R groups at Z are found in the interior of the fold rather than on the surface facing the water. (1 point)
A full-credit answer: Water’s partial charges are attracted to charged and polar R groups but find nothing to pull on in nonpolar ones, so the chain folds with its nonpolar R groups clustered together away from the water, in the interior, and its polar and charged R groups facing the water.
Check the box for each point your answer earns
Accept: 'nonpolar R groups are hydrophobic, so water excludes them and they gather in the interior (a hydrophobic interaction)'.
Do not award for 'nonpolar groups repel water', or for 'nonpolar groups are attracted to each other' with no reference to water.
Common slip: Saying nonpolar groups ‘repel water’ or ‘attract each other’ with no water in the story. Water excludes them; that is what pushes them together inside.
(d) The protein is warmed gently, enough to break the interactions at W, Y and Z while leaving the S–S link at X and every peptide bond intact. Explain what the protein loses when those interactions break, and why that stops it doing its job even though its amino-acid sequence is unchanged. (1 point)
A full-credit answer: The weak interactions, the backbone hydrogen bonds at W, the ionic interaction at Y and the hydrophobic interaction at Z, hold the fold.
When they break, the chain unfolds and loses its three-dimensional shape, and the two chains no longer fit together.
A protein’s function depends on its shape, so the function is lost, while the covalent peptide bonds and the primary structure survive.
Check the box for each point your answer earns
Accept: 'the shape is lost, and the job depends on the shape', with at least one of the broken interactions named.
Do not award for 'the peptide bonds break' or 'the sequence changes'.
Common slip: Saying the peptide bonds break or the sequence changes. Gentle warming breaks only the weak interactions; the chain and its order of amino acids survive, and the shape is what is lost.