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USC Invitational — Protein Modeling Part 3

Protein Modeling · Division C · USC Invitational · 2025

45 questions · 123 points · 50 min· 1 question from the original omitted

Original test source

You will have 50 minutes to complete this section along with Part II. Please do not write or mark up this test booklet. You may take apart these pages as long as you return them to us complete and in order. Please write your school name (including team name if your school has multiple teams) and number in the marked space at the top of each answer sheet. Please mark your answers and show work on the answer sheet provided, in the designated spaces provided. Any answers, work, or calculations written on the test document will not be scored. Three tiebreaker questions are marked on the test. In the event that we exhaust all three questions to break a tie, additional tiebreaker questions will be selected by random number generator. Good luck and have fun!

Multiple Choice:

Mark only the letter of your answer choice in the space provided on the answer sheet. Answers marked on this test document will not be scored. There is only one correct answer for each multiple choice question.

Question 1

2 pts

Which of the following amino acids is NOT chiral?

Question 2

2 pts

Which of the following amino acids does NOT have a ring structure in its sidechain?

Question 3

2 pts

A small molecule binds to an enzyme and induces a conformational change that does not impact the enzyme’s active site, but still causes a reduction in enzyme-substrate interaction. Which type of inhibition is this?

Question 4

2 pts

A peptide binds to an enzyme and induces a conformational change that rearranges the enzyme active site, causing a severe reduction in enzyme-substrate interaction. Which type of inhibition is this?

Question 5

2 pts

Which of the following is a way to successfully evade competitive enzyme inhibition?

Question 6

2 pts

Only one amino acid sidechain exists that contains:

Question 7

2 pts

How many amino acids are in each turn of a conventional alpha helix?

Question 8

2 pts

What is the rise distance of a conventional alpha helix turn?

Question 9

2 pts

Which of the following is not a zinc finger fold group?

Question 10

2 pts

How many base pairs are typically recognized by a classic zinc finger binding motif?

Question 11

2 pts

Which of the following best describes how zinc fingers interact with DNA?

Question 12

2 pts

Which of the following ions would most likely be able to replicate the effect of zinc in a Zinc Finger Protein?

Structure Spectacular. Select the structural category that best describes the given protein feature and mark the letter of your answer choice in the space provided on the answer sheet. Answers marked on this test document will not be scored. There is only one correct answer for each of the following questions.

Letter Legend for #13-20: a) primary b) secondary c) tertiary d) quaternary

PassageFor questions 13–20

Letter Legend for #13-20: a) primary b) secondary c) tertiary d) quaternary

Question 13

2 pts

Hemoglobin dimerizing to interact with red blood cells

Question 14

2 pts

Disulfide bond

Question 15

2 pts

Sequence: LPLTGGSG

Question 16

2 pts

Peptide bond

Question 17

2 pts

Hydrophobic core

Question 18

2 pts

Enzyme-catalyzed isopeptide bond

Question 19

2 pts

Structural element in the image above with the arrow labeled “#19”

Question 20

2 pts

Structural element in the image above with the arrow labeled “#20”

Free Response

Write your response in the space provided on the answer sheet. Answers, explanations, and work marked on this test document will not be scored. For calculations, show work and box your final answer.

Question 21

3 pts

What is the role of zinc in Zinc Finger Proteins?

Question 22

3 pts

Why is methionine the start codon?

PassageFor questions 23a, 23b, 23c

Alex, along with almost 5 million other Americans, has a peanut allergy. When a birthday cake is served at a friend’s birthday party, Alex hesitates to have any because of the peanut risk. But by some stroke of luck, his friend happens to have a mass spectrometer in his basement! (10 points total)

Question 23a

6 pts

Briefly (3 sentences or less) design a mass spectrometry experiment that Alex could use to determine whether the cake contains any peanuts.

Question 23b

1 pt

Could Alex also use an SDS-PAGE gel to identify the presence of peanuts in the cake? Yes or no?

Question 23c

3 pts

In the mass spec data, what entity (broadly speaking) should Alex look for to determine whether the cake contains peanuts?

PassageFor questions 24a, 24b, 24c

The Kaiso Zinc Finger Protein structure (PDB 4F6M) that you modeled prior to this tournament was obtained by x-ray crystallography. (16 points total)

Question 24a

4 pts

Explain how and why proteins can form crystals.

Question 24b

6 pts

The researchers who found the crystal structure also solved a structure using a different method, NMR spectroscopy, which collects a bundle of different detected structures that all result from the protein’s motion in a solution environment. What information might this give us that crystallography does not? (Second tiebreaker question)

Question 24c

6 pts

The Kaiso Zinc Finger Protein structure was obtained to a resolution of 2.40 angstroms. What does “resolution” mean in this context, and what does it tell us about the quality of the protein structure?

PassageFor questions 25a, 25b, 25c, 25d, 25e

Explain each of the following steps of cryo-EM in one brief sentence: (2 points each, 10 points total)

Question 25a

2 pts

Freezing samples on grids

Question 25b

2 pts

Taking images/videos on microscope

Question 25c

2 pts

Particle picking

Question 25d

2 pts

Creating 2D class averages

Question 25e

2 pts

Creating a 3D reconstruction (Third tiebreaker question)

PassageFor questions 26a, 26b, 26c

A common practice for research with in vitro (reconstituted) protein reactions is to add a reducing agent such as DTT or BME. (10 points total)

Question 26a

3 pts

Why may some researchers add reducing agents to in vitro protein reactions?

Question 26b

3 pts

What amino acid residue are they typically targeting with it?

Question 26c

4 pts

Would a reducing agent be useful for a reconstituted Zinc Finger Protein reaction? Why or why not?

PassageFor questions 27a, 27b, 27c, 27d, 27e

Everyone makes mistakes, including test writers! When writing this test, one of your test writers made five statements, shown in parts a-e. Your other test writer, however, points out that the first test writer was incorrect in many ways, but won’t tell them how. Can you help them figure out where it all went wrong? For each statement shown in parts a-e, state whether the statement is correct or incorrect. If it is incorrect, write a correct version of the sentence. (15 points total)

Question 27a

3 pts

The energetic barrier required for enzyme activity is called the actuation energy.

Question 27b

3 pts

Folded proteins are more energetically favorable than unfolded proteins.

Question 27c

3 pts

A map of a protein’s secondary structural elements is called a topology map.

Question 27d

3 pts

Protein denaturation is caused by the breaking of isopeptide bonds.

Question 27e

3 pts

Proteins are stabilized by salt bridges that form between two residues of similar charge.

PassageFor questions 28a, 28b, 28c

Alice is designing an experiment to identify which residues on a Zinc Finger Protein are a part of the active site. She has a hunch that an arginine in the core of the protein may be involved in enzymatic activity. (10 points total)

Question 28a

3 pts

Alice wants to mutate the arginine to another amino acid in an attempt to disrupt its activity and determine whether the arginine is essential for protein function. Name 3 amino acids that would disrupt the arginine function if mutated to them.

Question 28b

2 pts

After mutating the arginine to the residues you suggested in part (a), she determines that the arginine is an essential residue for protein function! She then wonders whether arginine is the ONLY residue that could function in that position. What other residue is most likely to fulfill the same function as the arginine?

Question 28c

5 pts

Alice does some further experiments and notices a pattern that active sites in enzymes often include a cysteine. Why might this be the case? (First tiebreaker question)

Question 30

6 pts

List three mechanisms by which zinc finger proteins regulate gene expression.