A3.1

Question 1 Single best answer 1 point

A coordinate file contains the line ATOM 193 CA ASP A1025 12.904 14.115 7.362 1.00 18.52 C. What does this line record?

  1. The carbonyl carbon atom of the aspartate in chain A
  2. The alpha-carbon atom of the aspartate in chain A
  3. A calcium ion on the aspartate in position A
  4. The alpha-carbon atom of the aspartate in position A

Question 2 Single best answer 1 point

A crystal-structure entry contains SEQRES records. What do they list?

  1. The residues of the protein chain that the model places
  2. The residues in the construct that differ from the natural one
  3. The sequence of the construct that was made and crystallized
  4. The sequence of the natural protein the entry is labeled with

Question 3 Single best answer 1 point

An enzyme works as a homodimer, but the ATOM lines of its crystal-structure entry list only chain A. Where, if anywhere, does the file record the dimer, and why?

  1. REMARK 350, because symmetry copies of the listed chain build the dimer
  2. REMARK 350, because it lists the second chain as residues not modeled
  3. Nowhere, because the ATOM lines would list both chains of a dimer
  4. SEQRES, because it lists the sequence again for the second chain

Question 4 Single best answer 1 point

A crystal-structure entry reports a resolution. What does this value measure, and which direction means more detail?

  1. The number of features resolved per ångström; a larger value means finer detail
  2. The smallest spacing the data resolve; a larger value means finer detail
  3. The smallest spacing the data resolve; a smaller value means finer detail
  4. How closely the model agrees with the data; a smaller value means finer detail

Question 5 Single best answer 1 point

A crystal-structure file lists one position for each atom of a protein. What does one such position represent, and why?

  1. The position that most molecules share, because the model keeps the majority conformation
  2. The position of one representative molecule, because the crystal is made of identical copies
  3. The average over the molecules in the beam during data collection, because each spot sums them
  4. The average over the molecules in the beam at one instant, because the exposure freezes them

Question 6 Single best answer 1 point

A classmate says the atom coordinates in a deposited crystal structure are read off an image of the protein. What is wrong with this account?

  1. The coordinates are a model fitted to the reflections, not positions read off an image
  2. Coarse-resolution coordinates are a model, but fine-resolution ones are an image
  3. The coordinates are separate measurements of each atom, not positions read off an image
  4. The coordinates do come from an image, but a blurred one, so each atom is placed roughly

Question 7 Single best answer 1 point

In one crystal-structure model, atom G has a lower B-factor than atom H. Which atom do the data place more precisely, and why?

  1. Neither, because B tracks the atom’s motion, a property of the molecule, not the data
  2. Atom G, because a lower B means the atom sits at that spot in more of the copies
  3. Atom H, because a larger B means stronger support from the data for that atom
  4. Atom G, because a smaller B means less blur in that atom’s position across molecules

Question 8 Single best answer 1 point

In one model, atom N has a B-factor several times that of atom M. How does the displacement \(u\) of atom N compare with that of atom M, and why?

  1. Larger by a bigger factor than B, because \(u\) grows as the square of B
  2. Larger by the same factor as B, because \(u\) measures the same blur as B
  3. Larger by a smaller factor than B, because \(u\) grows as the square root of B
  4. Larger by a smaller factor than B, because \(u\) measures the blur along one axis

Question 9 Single best answer 1 point

In one model, atom K has a low B-factor. You measure its distance to atom V, which has a high B-factor, and its distance to atom W, which has a low B-factor. Which distance do the data fix less tightly, and why?

  1. Neither; the entry’s resolution sets one coordinate error, so both are known equally well
  2. Neither; atom K anchors both distances, so its blur sets how well each one is known
  3. The distance to V, because V is the more blurred atom of the pair and limits the distance
  4. The distance to V, because a high B marks an atom the model has put in the wrong place

Question 10 Single best answer 1 point

Which parts of the HIV-1 protease active site does each of its chains supply?

  1. Each chain supplies one catalytic aspartate, and one of the chains supplies the flap
  2. Both catalytic aspartates come from one chain, and each chain supplies one of the flaps
  3. Each chain supplies one catalytic aspartate and one flap, so the two halves form one active site
  4. Each chain supplies one catalytic aspartate and one flap, so each chain makes its own active site

Question 11 Single best answer 1 point

Peptides with the sequences of residues 1-4 and 96-99 of HIV-1 protease inhibit the enzyme. How do the peptides inhibit it?

  1. They bind the dimer away from its active site and distort the site’s shape
  2. They sit in the active site, so they compete with the substrate for it
  3. They hold the dimer’s flaps open, so the site cannot grip its substrate
  4. They stop the two chains from pairing, so the active site is never assembled

Question 12 Single best answer 1 point

A two-chain entry of HIV-1 protease numbers chain A from 1 and chain B from 101. Which residue of chain B is equivalent to Leu 97 of chain A, and why?

  1. Leu 97, because equivalent residues in the two chains carry the same number
  2. Leu 197, because it sits at the same sequence position in the partner chain
  3. None, because chains numbered from different starts do not share one sequence
  4. Leu 197, because entries number a second chain 100 above the first by convention

Question 13 Single best answer 1 point

An HIV-1 protease entry labeled wild-type carries the substitution Q7K. Why does the crystallized protein carry it, and where does the file flag it?

  1. It blocks a site where the protease would cut itself; SEQADV lines flag it
  2. It blocks a site where the protease would cut itself; SEQRES lines flag it
  3. It was selected by an inhibitor as a resistance change; SEQRES lines flag it
  4. It was selected by an inhibitor as a resistance change; SEQADV lines flag it

Question 14 Single best answer 1 point

Substrate-bound entries of HIV-1 protease, such as 1F7A, carry the substitution D25N. Why was the enzyme made with this change?

  1. Asn25 is the residue the virus carries, so the change restores the natural protease
  2. Asp25 lets a lone chain cut too, so the change keeps lone chains from cleaving the substrate
  3. Asn25 helps the molecules pack, so the complex forms crystals that diffract better
  4. Asp25 does the cutting, so an unchanged protease would cleave the substrate it holds

Question 15 Single best answer 1 point

Two unliganded entries of one protein differ widely in flap-tip position, with low tip B-factors in both. Their sequence records match, their symmetry mates sit far from the flaps, and one entry’s R-free sits far above its R-work. Which causes of the disagreement remain open?

  1. Real state and model error; the contact and sequence checks exclude the other two
  2. Real state, crystal packing, and model error; the sequence check excludes the construct
  3. Model error; the large R-free gap shows one model is wrong, excluding the other three
  4. Real state; a wide shift at low B-factors excludes the other three causes
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