Passage Review: miRNAs and the transmission of genetic information to proteins, Part II

Note: the following post assumes intimate familiarity with Part I of this series.

The method I’m employing to analyze this passage is so powerful, I don’t even need to reproduce the passage here to answer the remaining questions. All we need is our carefully constructed passage map:

Paragraph 1:

Paragraph 2:

PDAC miRNA poorly understood

Paragraph 3:

EMT ↑ ⟼ metastasis ↑

EMT cells: adherent, polar ↓ ⟼ migratory ↑ = metastatic

miR-200 ↑ ⟼ TFs ZEB1/2 ↓ ⟼ EMT↓

E-cad ↑ ⟼ adherent, polar ↑ ⟼ EMT↓ ⟼ metastasis ↓

MI: does miR-200 ↑ ⟼ Epithelial ↑?

Figure 1:

E-cadherin: sum / mean miR-200b ↑ ⟼ E-cad ↑

miR-200b ↑ ⟼ ZEB1 ↓ [WEAK]

miR-200b ↑ ⇏ ZEB2

Paragraph 4:

Prostate CA ↑ ⟼ miR-34a ↓

miR-34a = E-cad ↑ ⟼ adherent, polar ↑ ⟼ EMT↓ ⟼ metastasis ↓

Figure 2:

Line 1: miR-34a ↑ ⟼ tumor growth ↓

Line 2: miR-34a ↑ ⟼ tumor growth ↓↓

Let’s dive into the next question:

Let’s restate the question stem and strip away the fluff: “this is also an example of secondary structure for nucleic acids…” We don’t care about hairpins or 70-sequence long stretches; all we care about is finding another example of secondary structure in nucleic acids. By the way, what is a nucleic acid, for MCAT purposes (I will never use the phrase “for MCAT purpose…” again because everything on this blog has the directed purpose of being relevant for the MCAT)?

A nucleotide is biomolecular monomer consisting of a five-carbon sugar, a nitrogenous base, and 1 to 3 phosphate groups. When we stitch at least 2 nucleotides together (how would we do this again? dehydration synthesis), we get a nucleic acid, like DNA or RNA. You probably have primary through quaternary structure down for proteins, but did you know you also need to keep that level of local organization in mind for nucleic acids, as well? Wikipedia saves the day:

Memorize this.

Primary = linear arrangement of nucleotides: literally the ordered sequence of letters

Secondary = base pairing interactions within the same molecule (e.g. complex interactions between base pairs along a single-strand of RNA, resulting in loops and knots) or between two polymers (e.g. DNA secondary structure base pairing in biological systems almost always results in a double helix)

Tertiary = 3D shape: so for DNA, we have the double helix, coming in three flavors, A-, B-, and Z-DNA (some resources consider that secondary structure). For RNA, any time we introduce a twist that affects the spatial extent, we count it as 3˚.

Quaternary = two distinct nucleic acids interacting (e.g. for RNA, ribosomes exhibit quaternary structural organization, since it is composed of multiple rRNA molecules) OR a nucleic acid-protein complex, such as a nucleosome (DNA wrapped in histones beads) or an amino acid-charged tRNA.

Now that you know this, the question is cake:

A. this is also an example of secondary structure for nucleic acids: DNA-RNA hybrid

If the RNA were to base pair with itself to form a loop or turn, it would count as secondary structure. But, we have an interaction with DNA, which means we have possible tertiary and even quaternary structure, depending on the reference you use (since there doesn’t seem to be consensus).

B. this is also an example of secondary structure for nucleic acids: alpha-helix in transmembrane receptors

Alpha-helices are secondary structures in PROTEINS. Eliminate.

C. this is also an example of secondary structure for nucleic acids: tRNA cloverleaf

When you read the word tRNA, this should pop in your head first:

The sequence of bases, from 5'-GCG…CCA-3', represents primary nucleic acid structure, whereas the loops, such as the anticodon loop, represent secondary structures. What else counts as secondary structures for RNA?

Answer choice C looks good. Keep it.

By the way, what would tertiary structure entail? The 3D spatial extent:

D. this is also an example of secondary structure for nucleic acids: disulfide bond in IgG

A disulfide bridge in an immunoglobulin (IgG) is an example of tertiary / quaternary structure for proteins. This wouldn’t even count as proteinaceous 3˚ structure, so drop this.

Next:

Let’s jump right in:

A. Prokaryotes aren’t great at making miRNA because: prokaryotes lack a true nucleus (so far so good) and are unable to produce mRNA (OK, no.)

Eliminate A.

B. Prokaryotes aren’t great at making miRNA because: most bacteria genomes contain no introns (yes, true) and are unable to produce RNA pol II (true!)

We know from our passage map that one way miRNAs are manufactured is from special transcriptional units or introns, so the first part of B works. Now, what about RNA pol II? You have to remember that transcription cannot occur in either prokaryotes or eukaryotes without RNA polymerase, but prokaryotes employ a single RNA polymerase (σ), whereas eukaryotes rely on 3 distinct types of RNA pol, I-III. So does our Frankenstein statement make logical sense taken as a whole? Prokaryotic miRNA production is handicapped by the fact that most prokaryotic genomes are intron-free, so they will not manufacture eukaryotic RNA polymerases either. Keep B.

C. Prokaryotes aren’t great at making miRNA because: prokaryote transcriptional units are simpler than those found in eukaryotes (probably true)

This is a weak Frankenstein because the question isn’t being answered. No where in our passage map does it indicate that the complexity of the synthesis precludes prokaryotic machinery. Drop C.

D. Prokaryotes aren’t great at making miRNA because: bacterial σ initiation factors bind tightly to RNA-pol and determine promoter interactions (true…but so what?)

Again, we are dealing with irrelevance. Why do you absolutely have to make these Frankenstein sentences? Because if you evaluate each answer choice as true or false without considering its context with the question stem, you could mistakenly choose an answer that may be true by itself, but has absolutely nothing to do with what is being asked. This brings me to my next tip:

Tip 7: be wary of “politician” answers

There will be times where you’re tempted to not use the tactic of concatenating your restated question stem with each answer choice, but that’s an invitation for potential failure. Tip 7 is exactly what it sounds like: avoid answers that don’t answer the question, which is a strategy employed by politicians.

When you read that, that should trigger you to recall what happened in Figure 2. In fact, that’ll be our restated question stem. Here are our choices.

A. Figure 2 strongly suggests: miR-34a expression promotes extensive cell death and necrosis.

Well we didn’t see the population ever reverse direction for the experimentally treated groups, so we can’t deduce that death and necrosis occurred.

B. Figure 2 strongly suggests: miR-34a is less effective at promoting cell death in Cell Line 1.

It’s hard to say if cell death is being promoted in either case. All we know is that growth is occurring in both lines and in both groups, it’s just that the experimental groups with the reintroduced miR-34a grow slower than their control counterparts. Let’s see what else is there.

C. Figure 2 strongly suggests: miR-34a exhibits potent anti-tumorigenic or anti-tumor-forming properties in PDAC cell lines.

So if the vector only plots show exponential growth, and we know that’s the definition of cancer — uncontrolled cell division — then if the cell cultures’ growth rates assume more linear or flat profiles, we have anticancer effects at play. In other words, we see how re-expressed miR-34a has anti-tumorigenic properties. C seems good. This is consistent with our passage map:

miR-34a = E-cad ↑ ⟼ adherent, polar ↑ ⟼ EMT↓ ⟼ metastasis ↓

D. Figure 2 strongly suggests: miR-34a is strongly downregulated in a majority of the PDAC cell lines.

This misconstrues the background information in Paragraph 4’s first sentence setting up the experiment plotted in Figure 2 with the actual results from Figure 2. Also Figure 2 doesn’t tell us anything about the degree of downregulation and simply shows very low miR-34a levels at Day 0. D is out.

Here’s a softball question:

Here, let’s reverse the flow of our restated Frankenstein sentences. We know that we want to maintain the epithelial cell phenotype, so we need something on the left side of this arrow in the square brackets that satisfies the relationship in the question stem:

[ ? ] ↑ or ↓ ⟼ Epithelial ↑

So now, let’s substitute each answer choice for the [ ? ] and see if that relationship is valid.

A. miR-34a ↓ ⟼ Epithelial ↑

we know that miR-34a = E-cad from Paragraph 4, so does decreased E-cad lead to the the epithelial phenotype? Definitely not. Remember:

E-cad ↑ ⟼ adherent, polar ↑ ⟼ EMT↓ ⟼ metastasis ↓

So if anything, we expect the opposite to occur.

B. ZEB1/2 ↑ ⟼ Epithelial ↑

What relationship did we capture for our TFs?

miR-200 ↑ ⟼ TFs ZEB1/2 ↓ ⟼ EMT↓

Once again, we noted the opposite of the relationship in our passage map than what was implied by the answer choice, so reject B.

C. E-cad ↑ ⟼ Epithelial ↑

The reason we rejected A is the reason we should strongly consider C:

E-cad ↑ ⟼ adherent, polar ↑ ⟼ EMT↓ ⟼ metastasis ↓

The beauty of the Altius method shines through again.

D. miR-200 ↓ ⟼ Epithelial ↑

We reject D for the same reason we rejected B: the implied relationship in the answer choice is inconsistent with our passage map relationships.

And that does it for this passage! I hope this was illustrative, and please check back regularly for additional demonstrations on the power of the Altius Test Prep solution.