Unit 1 · Practice for the Topic 1.7 end-of-topic test
You’ve gone through everything in this topic. The summary video below recaps it all, so you’re ready for the questions.
Watch first: Proteins, summed up
Amino acids, the chain, the four levels of folding, and why shape is the job.
The drawing shows one amino acid with the four groups on its central carbon numbered 1 to 4.
Which numbered group is the carboxyl 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?
A student writes: “A peptide bond forms between the R groups of two neighboring amino acids, and a water molecule is taken in as it forms.”
Which statement corrects the student?
A cell builds a polypeptide of 150 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 of 30 amino acids are identical except that the amino acids at positions 3 and 5 are exchanged with each other. Both chains have the same length and the same list of amino acids.
Do the two polypeptides have the same primary structure, and what should be expected of their shapes?
The model below shows a stretch of one polypeptide coiled into a spiral, with dashed lines running from one turn to the next.
What is this coiled stretch, and what are the dashed lines?
The model below shows two R groups of a folded protein that are far apart along the chain but sit close together. One ends in an –OH group; the other ends in a C=O group. A dashed line runs from the hydrogen of the –OH to the oxygen of the C=O.
Which interaction is drawn, and which level of structure does it help hold?
A polypeptide floats in the watery inside of a cell. Along one stretch of the chain, ten amino acids in a row carry R groups made only of carbon and hydrogen.
Where will that stretch most likely end up when the chain folds, and why?
A person’s fever climbs to 43 °C, and many of the proteins in their cells stop working. After the fever passes, some of those proteins stay tangled together and stay out of action.
What did the heat most likely do to those proteins?
In a protein that sits in water, an R group carrying a full negative charge attracts an R group carrying a full positive charge on a distant part of the chain, and this interaction holds one part of the fold in place. In a variant of the protein, the negatively charged amino acid is replaced by an amino acid with a nonpolar R group. Everything else is unchanged.
What is the most likely effect of the substitution?
(a) Identify the level of structure formed by the stretches lying side by side, and name the arrangement. (1 point)
A full-credit answer: The stretches lying side by side are secondary structure.
The arrangement is a beta pleated sheet.
Check the box for each point your answer earns
Do not award: alpha helix, or tertiary structure.
Common slip: Calling the side-by-side stretches tertiary structure because they are folds. Folding held by backbone-to-backbone hydrogen bonds is secondary structure.
(b) Describe one hydrogen bond in these sheets: name the two backbone groups it joins, 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: The hydrogen bond joins a backbone N–H group on one stretch to a backbone C=O group on the neighboring stretch.
The H of the N–H group is δ+, because the N pulls the shared electrons toward itself.
The O of the C=O group is δ−, because the O pulls the shared electrons toward itself.
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: ‘partly positive’ and ‘partly negative’ for δ+ and δ−; the reason for the partial charges is not required.
Do not award: a hydrogen bond between R groups, the partial charges reversed, or the N named as the atom that attracts the O.
Common slip: Placing the hydrogen bond between R groups. In a sheet the R groups point above and below the sheet; the bonds that hold the stretches together join a backbone N–H group to a backbone C=O group.
(c) Explain how the order of amino acids in the silk chain decides the shape the chain takes. (1 point)
A full-credit answer: The order of amino acids is the chain’s primary structure; it sets where each kind of R group sits along the chain, so it sets which interactions can form and where the chain folds.
A different order would put different R groups in each place and give a different shape.
Check the box for each point your answer earns
Accept: ‘primary structure determines shape’ provided the R groups are given as the link.
Do not award: ‘the amino acids decide the shape’ with no mention of order or R groups.
Common slip: Saying the shape depends on which amino acids are present. The same twenty in a different order give a different shape; it is the order that matters.
(d) Predict what happens to the sheets in the variant protein, in which every third R group in those stretches carries a full charge. (1 point)
A full-credit answer: In the variant, water is pulled toward the charged R groups, so those stretches are held in contact with the water instead of packing side by side away from it, and the sheets form poorly or fall apart; the chain folds differently in that region.
Check the box for each point your answer earns
Accept: ‘the charged groups pull that part of the chain toward the water and the sheet does not form properly’.
Do not award: no change, or the chain breaking.
Common slip: Predicting no change because the backbone is the same. The backbone is the same, but the R groups are what water sorts, and a charged R group is treated very differently from a nonpolar one.
(e) Support the claim that the variant thread would be weaker, using the relationship between a protein’s shape and its job. (1 point)
A full-credit answer: A protein’s shape is what lets it do its job.
The thread is strong because many sheets pack together into a tough fiber.
In the variant the sheets are disrupted, so the packed fiber cannot form as before.
So the thread is weaker.
Check the box for each point your answer earns
Accept: ‘shape is the job’ applied to the disrupted sheets.
Do not award: ‘it is weaker because the amino acids are different’ with no link through shape, or the claim restated with no evidence.
Common slip: Going straight from ‘different amino acid’ to ‘weaker thread’. The step in between is the shape: the R groups change the interactions, the interactions change the fold, and the fold is what does the job.
(a) Describe the levels of structure that a molecule of insulin has. (1 point)
A full-credit answer: Each chain has primary structure (its order of amino acids), secondary structure (coils and sheets held by backbone hydrogen bonds) and tertiary structure (its overall fold held by R-group interactions); because two separately folded chains fit together, insulin also has quaternary structure.
Check the box for each point your answer earns
Accept: the four levels named with quaternary tied to the two chains.
Do not award: quaternary structure denied, or ‘all four levels’ with no reason for the fourth.
Common slip: Denying quaternary structure because insulin is small. Quaternary structure needs two or more separately folded chains fitted together, and insulin has two.
(b) Explain why the arrangement of hydrophobic R groups along each chain matters for the way the chain folds in the watery blood. (1 point)
A full-credit answer: Water is attracted to charged and polar R groups and not to nonpolar ones, so a chain in water folds with its hydrophobic R groups clustered in the interior and its polar and charged R groups facing the water.
Wherever the nonpolar R groups sit along the chain, the chain tucks inward there, so their arrangement sets where the chain folds.
Check the box for each point your answer earns
Accept: ‘the nonpolar R groups end up inside, away from water, so where they are decides the fold’.
Do not award: hydrophobic R groups on the surface, or the fold explained by the backbone alone.
Common slip: Putting the hydrophobic R groups on the outside. Water excludes them, so they gather in the middle of the fold.
(c) Describe what the heat in the car did to the shape of the insulin molecules, and explain why they stopped working. (1 point)
A full-credit answer: The heat broke the weak interactions holding each fold, the hydrogen bonds, ionic interactions and hydrophobic interactions, so the chains unfolded and clumped together with one another, which is what turned the liquid cloudy.
The peptide bonds and the order of amino acids survived, but the molecules lost their shape, and a protein’s shape is what lets it do its job, so the insulin no longer works.
Check the box for each point your answer earns
Accept: ‘the fold is lost but the sequence survives, and without its shape it cannot work’.
Do not award: peptide bonds broken, or the sequence changed.
Common slip: Saying the heat broke the protein into amino acids. Peptide bonds are covalent and survive; the fold, held by weak interactions, is what the heat destroyed.
(d) Support the claim that the insulin stays out of action after the vial is cooled again. (1 point)
A full-credit answer: The cloudiness shows that the unfolded chains have clumped together.
Cooling does not pull the clumped chains apart, and it does not fold each one back into the particular shape it had.
So the shape stays lost.
A protein’s job depends on its shape, so the insulin stays out of action, just as a cooked egg white stays solid when it cools.
Check the box for each point your answer earns
Accept: comparison with cooked egg white staying solid, with the clumping named.
Do not award: ‘the peptide bonds are gone’, ‘the protein was used up’, or the claim restated with no evidence.
Common slip: Expecting the fold to return when the interactions can form again. The clumped chains are stuck against one another in the wrong places; the original shape does not re-form.