Next Step Full Length 10, Bio/Biochem Passage 7

Session 127

We are joined by Clara of Next Step Test Prep as we break down some more of Next Step Test Prep’s full length then exams. This week, we’re in the Bio/Biochem section, Passage 7, which is all about white blood cells, viruses, and bacteria and how they respond in the body of mice.

Just to give you an idea, every science section has ten passages as well as four sets of discrete questions.

[02:25] Passage 7

TLR is our receptors on leukocytes that recognize viral and bacterial components causing signaling to generate, among other things, proinflammatory cytokines. TLR4 is a TLR that recognizes lipopolysaccharide (LPS), a glycolipid present on gram-negative bacterial membranes. Signaling through TLR4 occurs when a ligand brings two TLR4 molecules together in a process called ligand-induced dimerization. A researcher who’s investigating use of synthetic TLR4 ligand as an adjuvant to enhance the immune response against a vaccine by stimulating cells release cytokines that enhance antibody responses by B cells. The researcher obtains purified TLR4, immobilize it to a surface and incubates the receptor with the synthetic TLR4 ligands, compounds A through D to measure affinity. The following results are obtained: Table 1 shows Dissociation Constants of Compounds A through D and Binding TLR4.

Clara says: The table also gives a Kd for each. And if the question asks about the Kd, your dissociation constants will come back as stable. If not, we don’t have to worry about it.

Experiment 1: The researcher then compares immune response against a synthetic agonist compared with an equal mass of live bacteria and purified lipopolysaccharide. By measuring mouse survival after a five-day inoculation. The live bacteria include pathogenic strains of E. coli and S. enterica both gram-negative and S. aureus, gram-positive.

Experiment 2: The researcher now wishes to explore the efficacy of a vaccine formulation with either a purified antigen present both on S. enterica and S. aureus were purified antigen plus TLR4 based adjuvant which is either compound B, C, or D. The purified antigen is normally a membrane-bound receptor on the bacteria. He vaccinates the mice. Two weeks post vaccination, he inoculates the mice separately with either S. enterica or S. aureus and measures survival after five days. The same amount of bacteria as in Experiment 1 is used.

[05:10] Clara Recommends

Clara recommends it’s a good idea not to reread the passage. And it’s a good thing that you won’t have time because, for passages like this, you don’t have to understand every word you read. A lot of smart students can get stuck here, worried they haven’t had studied enough. But just stop right here and look for the keywords and phrases out of this such as immune system and adjuvant. We know there are these specific types of bacteria mentioned throughout the package. You can also highlight the key terms and memorable phrases from each paragraph then just move on. Just go back to the passage when you need to.

[05:55] Question 35

What is not a possible explanation of the survival for mice challenged with S. aureus in Experiment 2?

  • (A) S. aureus is a gram-positive bacteria.
  • (B) The antigen is only expressed on S. enterica.
  • (C) S. aureus subverts an immune response against it.
  • (D) TLR4 signaling has minimal effect.

Clara’s insights:

The answer here is B. It’s important to recognize that this is a “not” question so three of these must be possible explanations for whatever the question is asking. We’re not given much information about what extent the survival occurs. Some mice may have survived and some may have died in the experiment. A was mentioned in the passage and whether that’s a possible explanation for survival, maybe. B says “only” and so it’s an extreme statement. So if you can prove that false, that gives you some information. Look back at the passage on Experiment 2, it talked about both S. enterica and S. aureus. So B is not true.

When answering questions of this nature, first of all, the answer choice has to be accurate. Secondly, the answer choice has to do whatever the question is asking with regard to the explanation. And B, just straight up, is not accurate, so it’s definitely not a possible explanation.

This does happen on the MCAT where you get an answer choice that contradicts information you know or in the passage. So you have to consider the passage to be our resource here.

[11:22] Question 36

What is the purpose of an adjuvant?

  • (A) It acts as a transcription factor.
  • (B) It binds antibodies.
  • (C) It increases protection granted by vaccine of a host against pathogens.
  • (D) It causes dimerization of receptors.

Clara’s insights:

The correct answer here is C. There are different ways you can go about this one. If you don’t have any knowledge of vaccines and what an adjuvant does, you can always go back to where they first mentioned it in the passage, where they directly tell us that an adjuvant enhances an immune response against a vaccine. It’s nice if you can get to this answer choice right away. But if you read the passage, you could get confused with the term dimerization. But that’s not the purpose of an adjuvant in general. Hence, C is correct.

[13:24] Question 38

The researcher isolates antibodies against S. enterica from the vaccinated mice who survived at the end of Experiment 2. Binding in an isolated antibody is mediated largely by a sequence in the CDR3 (complementary determining region) of the antibody. He sequences the protein and determines that binding is mediated by the sequence lysine-lysine-arginine-glycine-aspartate-glycine-lysine-serin-lycine. What region of TLR4 is this antibody most likely to bind?

  • (A) Cytoplasmic domain
  • (B) Transmembrane domain
  • (C) Ligand binding site of TLR4
  • (D) Extracellular domain

Clara’s insights:

This has nothing to do with TLR 4 and everything to do with the sequence of amino acids they gave us. If you look at the actual sequence, these are very polar amino acids for the most part. Lysine and arginine are charged and super polar. So as soon as you see these polar amino acids, you can think that polar is going to bind other polar things. So this antibody is most likely to bind to a region that is rich in polar residues.

(A) Cytoplasmic domain is pretty polar but it’s also in the inside of the cell so that’s not where the antibody is going to bind. So A is out. Transmembrane domain is nonpolar because it’s buried inside the lipid bilayer. Answer choice C is kind of weird as there’s no reason we can say it’s not C in this question. But it’s probably a nonpolar region. And then as you go to (D), and always in any protein in the body, the extracellular domain will be relatively rich in polar residues. Hence, D is the correct answer here.

[18:07] Question 39

Signaling through TLR4 occurs when a ligand brings two TLR4 molecules together in a process called ligand-induced dimerization. TLR4 as a homodimer then recruits proximal adaptor molecules leading to a phosphorylation cascade that ultimately results in NFKB import into the nucleus. NFKB ultimately results in the change of cellular proteins leading to a proinflammatory phenotype. What type of molecule is NFKB most likely to be?

  • (A) Translation factor
  • (B) Transcription factor
  • (C) Protease
  • (D) Kinase

Clara’s insights:

The correct answer here is B. Protease and Kinase are both enzymes where protease will break down a protein while a kinase will phosphorylate a protein. But neither of the two would be expected to happen in the nucleus and you wouldn’t say it results in the change of cellular protein on a large scale. So now we’re left with A and B. Transcription happens in the nucleus whereas translation happens in the cytosol, on ribosomes, or ribosomes bound to the ER. And since the question says NFKB is imported into the nucleus, so it has to be (B) Transcription factor.

Transcription is an earlier stage in the process. Basically, we’re trying to take our DNA which is storage material permanently located in the nucleus. And we’re trying to get protein out of it. Whatever proteins we make from that, DNA will impact the phenotype of the cell. This happens in two stages. First is transcription where DNA is transcribed into RNA and then RNA is processed and shifts out of the nucleus where it would degrade. But before it degrades, it’s picked up by the ribosome and turn that RNA into protein.

In this question, we’re affecting transcription on the transcription level so the transcription would be that where we’re reading DNA, making this RNA from that template.

[23:15] Next Step Test Prep

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