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Why Does the USMLE Step 1 Care if a Virus Has +RNA or -RNA?

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by Alec Palmerton, MD in Cheat Sheet

Here, I share both the tools and knowledge I used to score a 270 on the USMLE Step 1 exam. How did I do it? Since the USMLE Step 1 exam tests your understanding and application of knowledge rather than memorization, the students who have the best understanding of the processes they learn will do the best.

As a teaser, I will start with the questions you will be able to answer by the end of this. By understanding these “pathogenesis to presentation” questions, where you can create a narrative between the pathophysiology to the way that they present, you will in fact be able to recall the related information involved without having to memorize it! Here are the questions:

  1. What does “naked viral genome infectivity” mean?
  2. Naked viral genome infectivity – what naked viral genomes are infective and why?
  3. What are the exceptions and why?

What is the process of transcription? What do you call the product of this?

DNA → RNA (specifically, mRNA, or “messenger” RNA)

What is the process of translation? What is the translation “start” signal?

mRNA → protein

AUG = start signal

What direction is RNA synthesized? (5’ → 3’ or 3’ → 5’)

5’ → 3’

What direction is RNA read? (5’ → 3’ or 3’ → 5’)

5’ → 3’

RNA processing (eukaryotes) - what are the major steps (3)

Capping on 5′ end (7-methylguanosine)Polyadenylation on 3′ end (~200 A’s)Splicing out of introns

What is the purpose of capping?

Recall that RNA is VERY easily degraded, so must PROTECT RNA

5′ cap – protect it from being degraded by exonucleases (“exo” because it cleaves RNA beginning from the “outside” – i.e. ends; as opposed to “endo”nucleases which cleave the RNA strands from the middle)

What is the purpose of and polyadenylation of RNA? What end does this occur at?

Recall: as long as the RNA persists in the cytosol, you can make proteins out of it. HOWEVER, you want to LIMIT the amount of proteins that you make from any one mRNA.

3′ polyA tail – the 5’ end of the RNA is protected by the 5’ cap. However, exonucleases will degrade the RNA starting at the 3’ end, thus having a longer 3’ “tail” will require MORE time for exonucleases to degrade the RNA.

Basically sets halflife, as it will take a while for exonucleases to degrade it

Initiation of translation - what is the mechanism?

Small subunit binds upstream on 5’ cap, then proceeds downstream until AUG (start codon) is encounteredProkaryotic small subunit: 30S. Eukaryotic small subunit: 40S.Joined by the large subunit, initiation factors (IFs), and the initiator tRNA (Met or fMet) enters the P-siteProkaryotic large subunit: 50S. Eukaryotic large subunit: 60S.Initiator tRNA is the only tRNA that can bind to the P-site; all others bind to A-site

What does it mean to be a +RNA virus?

Virus whose RNA genome can be translated directly into a protein.

Recall that in RNA, messenger RNA (mRNA) is what can be translated directly into a protein, while the complementary strand itself does not code a protein to be synthesized – but it is “complementary” to a strand that can be. Thus, +RNA viruses are those whose genome is essentially mRNA.

What does it mean to be a -RNA virus?

Just like +RNA is mRNA, if the virus is -RNA, its genome cannot be translated directly into a protein.

RNA polymerase – what is the alternative term?

DNA-dependent, RNA polymerase

In other words, it READS DNA, and PRODUCES RNA

Alternative term for what? (HINT: turn this into a “reverse” Anki card)

Reverse transcriptase – what is the alternative term?

RNA-dependent, DNA polymerase

In other words, it READS RNA, and produces DNA

Alternative term for what? (HINT: turn this into a “reverse” Anki card)

DNA polymerase – what is the alternative term?

DNA-dependent, DNA polymerase

In other words, it READS DNA, and produces DNA

Alternative term for what? (HINT: turn this into a “reverse” Anki card)

What would you call the enzyme that turns –RNA → +RNA?

RNA-dependent RNA polymerase

What action would this have?
*NOTE: despite the fact that the polymerase is still technically an RNA polymerase, it is NOT what is commonly referred to as an “RNA polymerase” in common parlance. “RNA polymerase” refers to a DNA-dependent RNA polymerase.

What does “naked viral genome infectivity” mean?

If I took the naked viral genome (i.e. ONLY the genetic material, and NOT the envelope/capsid) and injected it into a cell, it could produce viral progeny

Wait!

It is strongly recommended that you attempt to answer the final questions by yourself first, before looking at the answers.  Remember, the USMLE Step 1 exam will test your ability to make connections on the spot, the more practice you have, the higher your score!  Then, when you think you might know the answer (or are completely stumped), look at the answers below!


Ready for the answers?

If I injected the naked viral genome of a dsDNA virus into a cell, could that cell become “infective” (i.e. produce viral particles)? Why or why not?

Typically, it IS infective. This is because the dsDNA can be recognized by our own DNA/RNA polymerases, so can be transcribed/translated by our own protein machinery.

Naked viral genome infectivity – what naked viral genomes are infective and why?

dnDNA (dsDNA can be recognized by our own DNA/RNA polymerases, so can be transcribed/translated by our own protein machinery)+RNA – infective because it’s basically mRNA (i.e. your small ribosomal subunit would recognize it, find the AUG start codon, and begin translation AS IF IT WERE YOUR OWN mRNA)

What are the exceptions to naked viral genome classes that are infective? Why?

dsDNA viruses CAN, except for Pox (requires own polymerase) and Hepadna (presumably because it is only partially dsDNA)

NOTE: ALL +RNA viruses’ naked genomes are infective

What naked viral genome classes are NOT infective? Why?

-RNA – recall that –RNA is NOT mRNA, but rather the complementary strand (i.e. you need an RNA-dependent RNA polymerase to convert it to mRNA to be translated)

ssDNA – also requires its own polymerase

What should you do next?

  1. Turn the narrative, “Pathogenesis to Presentation” questions into Anki cards by copy/pasting the question/answer into the “Front” and “Back” fields in Anki.  Do the same for the fundamental facts that you were unfamiliar with, to maximize your chances of USMLE Step 1 success!  Remember: the USMLE is a test of understanding, so the better you can understand these questions, the better your score!
  2. Add reverse cards when appropriate to your Anki cards
  3. Re-word the questions/explanations as desired, and BOLD the important text to make it easier to review in the future
  4. Learn something new?  Something unclear?  Comment below!
  5. If you liked this post, please consider sharing it on Facebook/Twitter!  I judge the utility of these posts by the number of comments / shares they receive, so if you’d like more, or would like a particular topic addressed, please let us know!
10 Comments
  1. RP says:

    dude i fucking hate your site. so goddamn clickbaity and a waste of my time.

  2. Chris says:

    I was under the impression that ssDNA could be infective, at least for parvovirus. It has those hairpin turns at the end of the strand, which act as primers for host DNA polymerase. The dependence explains why parvo can only infect cells in the S phase, which explains its penchant for affecting erythroblasts (but not erythrocytes) and causing transient aplastic anemia. Maybe its a small point, but I thought that was a pretty cool set of connections, in the vein of your “trying to think about how stuff works.”

    Anyhow, you are a kindred spirit in your approach to things (being preoccupied with mechanisms and I have also earnestly said “anki changed my life”) and its heartening to see how successful you were. You have some really great material on this site, so thanks for your hard work and thoughtful problems (unfortunately there are so few problem sets in med school).

    1. Chris says:

      Also giving all of your posts with such click bait-esque titles is hilarious

      1. Yousmle says:

        Hi Chris!

        Thank you so much for your kind message! You definitely are a kindred spirit. I had never thought about that before about parvovirus, but it makes complete sense! It is sad that so much of medicine is taught via rote memorization, but remember, the more you can stay true to your desire to learn mechanisms, and understand the body, the better you will do. I truly believe this.

        Best of luck! I hope to hear from you again soon!

        Alec

  3. JoeFlo says:

    Hi, first of all thank you for all of your amazing advice. Like so many other students, I wish I had found this site months ago! After finding it today I have already read many of your very helpful articles and I have started making pharm flashcards on Anki. It has been the death of me and I am excited to master it with Anki’s help. I signed up for your email but I can not find where to get the micro flashcards. Can you please tell me how to get them? Thank you for all of your help!

    1. Yousmle says:

      Hi Joe,

      Thank you so much for your kind words! I think everyone who has studied for Step 1 wishes they had known a ton of things – I certainly felt the same way, and as such, try to pass on as much of that info through the blog and students I tutor =).

      It can take several days for the starter deck e-mail to be sent out, but I just just checked, and it should have been sent. If you have any problems accessing it, please let me know.

      Best of luck with your USMLE preparations, and I encourage you to leave feedback/comments on the site!

      Take care,
      Alec

  4. lee says:

    Man, how do we get ur micro deck? This is really good stuff btw.

    1. Alec Palmerton, MD says:

      Hi Lee, thank you for your question. You can get a copy of my "Starter" micro deck by signing up to get updates by e-mail (which I would recommend doing anyway if you like the content!). I appreciate that you find this helpful. Can I ask what in particular is most helpful, so that I can know how best to improve the content to help?

  5. John says:

    Really good.

    1. Alec Palmerton, MD says:

      Thank you so much for the feedback! I hope you found it useful!!

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Want FREE Cardiology Flashcards?

Cardiology is key for impressive USMLE scores. Master cardiology from a Harvard-trained anesthesiologist who scored USMLE 270 with these 130+ high-yield flash cards. You’ll be begging for cardio questions - even if vitals make you queasy.

Subscribe