Biochemistry Assessment #2

The USMLE has zero interest that you know of something weird called the Gαq-p63RhoGEF-RhoA/Rac1 pathway.¹  But they would want you to notice that within that obscure name it says Gαq.

• Gαq G-protein activation ↑ diacylglycerol.²
• Gαs G-protein activation ↑ cAMP.³
• Gαi G-protein activation ↓ cAMP.³

Then you need to consider, “Is the G-protein they’re talking about more active or less active?”

• ↑ GTPase activity → shuts off G-proteins.⁴
• ↓ GTPase activity → more G-protein activity.⁴

Therefore impaired GTPase activity means increased G-protein activity.

So for this vignette, we have a Gαq G-protein that is always active. That means ↑ diacylglycerol.

If you’re seeing this concept for the first time, it might seem low-yield and esoteric, but it’s actually high-yield for the USMLE Step 1 and you will get at least one G-protein question on your exam.

Bottom line: Gαq ↑ diacylglycerol. Gαs ↑ cAMP. Gαi ↓ cAMP. ↑ GTPase activity → shuts off G-proteins. ↓ GTPase activity → more G-protein activity.

1) https://www.ncbi.nlm.nih.gov/pubmed/24008316

2) https://www.ncbi.nlm.nih.gov/pubmed/24608858

3) https://www.ncbi.nlm.nih.gov/books/NBK464633/

4) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC16321/

Dapagliflozin is an SGLT2 inhibitor used in the treatment of T2DM. It functions by blocking glucose reabsorption in the PCT of the kidney.¹

The SGLT2 transporter functions via the mechanism of secondary active transport.²

“Active transport” means energy is required for the process to occur.

In primary active transport, ATP is used directly to mediate the transport (e.g., Na/K-ATPase pumps).³ In other words, the movement of sodium and potassium across a membrane is enabled directly by ATP.

In secondary active transport, ATP is used indirectly because it is the favorable gradient created by the primary ATPase that is used to drive the movement of solutes from a secondary (different) transporter. In the case of SGLT, glucose is transported against its gradient, but sodium is transported heavily with its gradient.

Carrier-mediated diffusion (aka facilitated diffusion) requires no energy and refers to a transporter protein or channel that simply allows a solute to move down its concentration gradient. An example is GLUT, which allows glucose to move across the basolateral membrane after it’s already crossed the apical membrane via secondary active transport.⁴

Group translocation is a method via which bacteria take up glucose. It involves various plasma membrane and cytosolic enzymes.⁵ You do not need to know this one for USMLE.

Phosphorylation-coupled transport may be seen as part of group translocation in bacteria.⁶ You do not need to know this one for USMLE.

Bottom line: Know the meaning of carrier-mediated transport, primary active transport, and secondary active transport for the USMLE.

1) https://diabetes.diabetesjournals.org/content/57/6/1723

2) https://www.sciencedirect.com/science/article/pii/S000527281000722X

3) https://www.ncbi.nlm.nih.gov/books/NBK537088/

4) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425736/

5) https://www.ncbi.nlm.nih.gov/pubmed/31214989

6) https://www.nature.com/articles/nature09939

Plasmids play a major role in carrying antibiotic resistance genes.^{1, 2, 3} This is HY on the USMLE.

Transduction refers to viral-mediated transfer of bacterial genes.⁴

Generalized transduction is when a phage particle (virus) enters a bacterial cell and, in its active lytic phase, packages any part of the bacterial chromosome into new phage particles. These new phage particles leave the cell and reinfect other bacteria, causing transfer of genes.⁴

Specialized transduction is when a phage particle enters a bacterial cell and then incorporates itself into the bacterial genome (lysogenic phase). Upon reemerging during a subsequent lytic phase, flanking bacterial chromosomal sequences are packaged into new phage particles.⁴

Rapid mutation patterns might explain the quickly evolving nature of bacterial genomes and ability to confer/lose resistance, but plasmid loss is far more likely a mechanism for reversion to antibiotic susceptibility.

Bottom line: Antibiotic resistance genes are most often carried on bacterial plasmids. Loss of plasmid is a mechanism via which bacteria may regain antibiotic susceptibility.

1) https://academic.oup.com/jac/article/73/5/1121/4822282

2) https://www.ncbi.nlm.nih.gov/pubmed/12878520

3) https://www.nature.com/articles/s41467-017-01532-1

4) https://www.ncbi.nlm.nih.gov/books/NBK21760/

Hexokinase is the first enzyme of glycolysis and is found ubiquitously. Glucokinase is the hexokinase variant in the liver and beta-islet cells of the pancreas.¹

Unlike hexokinase, glucokinase is induced by insulin and inhibited by epinephrine, cortisol, glucagon, and growth hormone.²

Insulin induces PFK2, not PFK1. PFK2 then acts as a positive allosteric regulator/inducer of PFK1 in glycolysis.³

There may be some evidence suggesting pyruvate kinase basal levels are sustained by the presence of insulin.⁴ However glucokinase is notably induced by insulin.

Glycogen phosphorylase is a catabolic enzyme. Its activity is suppressed in the presence of increased insulin levels.⁵

Bottom line: Insulin induces glucokinase. It does not induce hexokinase. Glucokinase is the hexokinase variant in the liver (and pancreatic beta-islet cells).

1) http://bip.cnrs-mrs.fr/bip10/glucokin.htm

2) https://www.sciencedirect.com/book/9780123919090/

3) https://link.springer.com/content/pdf/10.1007%2FBF00404065.pdf

4) http://www.jbc.org/content/257/18/10617.full.pdf

5) https://www.ncbi.nlm.nih.gov/pubmed/9038862

Before you freak out about the verbosity of such question stems, take a step back and remember that the USMLE often embeds a simple concept within them

In this scenario, we had an insertion/deletion process occur in the absence of DNase. But then once DNase was added, this process did not occur.

So the question becomes, “Which of the following processes would be disrupted by DNase?”

Slipped strand mispairing refers to an error in DNA replication where an insertion or deletion of small DNA repeats occurs at sites rich in tandem repeats, which are regions of genomic instability.¹ In other words, if a DNA sequence is rich in, e.g., AGTC repeats at a particular location, the chance of insertions or deletions occurring within this repeat sequence is increased because of slipped strand mispairing.²

• When DNA polymerase encounters an unstable tandem repeat sequence, it dislodges from the template strand.³
• The newly synthesized strand then detaches from the template strand and pairs with a different nearby tandem repeat on the template strand.
• DNA polymerase then reattaches and resumes replication.
• Depending on where the newly synthesized strand reattaches determines whether insertion(s) or deletion(s) occur.

Now for the DNase component:

During the phase in which the newly synthesized DNA strand detaches/reattaches from the template strand, the phosphodiester bond formation process is susceptible to degradation if a DNase enzyme is present.⁴ This means slipped strand mispairing could explain the mechanism seen in the question stem.

Conjugation is a process through which bacteria join using a pilus, often resulting in a plasmid transfer.⁵ Gene transfer would be protected from DNase.⁶

Plasmid disintegration (i.e., loss of plasmid) is notably a mechanism explaining why an antibiotic-resistant bacterial strain may revert to susceptibility.⁷

It should also be noted that transformation (not an answer choice here) is also susceptible to DNase. This is when bacteria take up genes directly from the extracellular space (i.e., the genes are not protected by any structure such as a pilus).

Bottom line: For the USMLE, if they ask you for which bacterial processes get fucked up when DNase is added to the medium, slipped stand mispairing and transformation are the answers. Even if you don’t fully understand the processes (or don’t care), memorize those answers in this context.

1) https://www.ncbi.nlm.nih.gov/pubmed/8809773

2) https://jb.asm.org/content/185/23/6990

3) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC125466/

4) https://www.sciencedirect.com/science/article/pii/S0065277616300529

5) https://www.ncbi.nlm.nih.gov/pubmed/7854127

6) https://jb.asm.org/content/jb/180/11/2901.full.pdf

7) https://www.nature.com/articles/s41467-019-10600-7

This boy has Duchenne muscular dystrophy.

It is an X-linked recessive condition caused by mutations in the dystrophin gene (DMD).¹

Dystrophin is a large cytoskeletal protein inside skeletal muscle that stabilizes the cytoskeleton with the extracellular matrix. Dystrophin binds to a transmembrane protein called beta-dystroglycan. The dystroglycan-dystrophan complex is necessary for normal skeletal muscle cell integrity.^{1, 2} 

Pseudohypertrophy of the calf muscles is a pathognomonic finding. This term refers to the fibroadipose deposition in the muscle that resembles muscular hypertrophy.³

Bottom line: There are innumerable question variants asked on the USMLE regarding Duchenne muscular dystrophy. You must know that it is X-linked recessive, that dystrophin is a cytoskeletal protein, and that Becker muscular dystrophy is a less severe form of Duchenne. I have a more detailed post in which I discuss plenty of factoids on Duchenne and Becker here (open in separate tab!).

1) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1299132/

2) https://www.sciencedirect.com/science/article/pii/S0959437X03000480

3) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3713639/

In a previous question, we discussed G-proteins broadly for the USMLE:

• Gαq G-protein agonism ↑ diacylglycerol.²
• Gαs G-protein agonism ↑ cAMP.³
• Gαi G-protein agonism ↓ cAMP.³

However in this question we’ve asked you to identify which G-protein corresponds to a receptor type (i.e., β2), and in turn knowing how agonism vs antagonism will change downstream cellular mediators.

The first-line treatment for an asthma attack is albuterol (aerosolized short-acting beta-2 agonist).

β2-agonism causes activation of gαs G-proteins, which ↑ adenylyl cyclase activity and ↑cAMP production.¹

Important G-alpha-q ligands: H1, α1, V1, M1, M3^{4, 5, 6, 7} (“HAVe 1 or 3 M&Ms”)

Important G-alpha-s ligands: β1, β2, β3, D1, H2, V2^{7, 8, 9, 10, 11}

Important G-alpha-i ligands: M2, α2, D2^{12, 13, 14} (“MAD 2s”)

Bottom line: Know the different G-proteins and their respective ligands. Yes, I know they’re annoying to memorize at first, but if you have any desire for a 245+ score on the USMLE you really should know them.

(Btw it took me a painful amount of time to source everything in this question. But let that be an indicator that I actually give a fuck about your learning.)

1) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574867/

2) https://www.ncbi.nlm.nih.gov/pubmed/24608858

3) https://www.ncbi.nlm.nih.gov/books/NBK464633/

4) https://www.ncbi.nlm.nih.gov/pubmed/11245606

5) https://www.ncbi.nlm.nih.gov/pubmed/9415716

6) https://www.ncbi.nlm.nih.gov/pubmed/18511496

7) https://www.sciencedirect.com/science/article/pii/B9780123809261100033

8) https://www.ncbi.nlm.nih.gov/pubmed/15703379

9) https://www.ncbi.nlm.nih.gov/pubmed/11238742

10) https://www.ncbi.nlm.nih.gov/pubmed/8961278

11) https://www.ncbi.nlm.nih.gov/pubmed/10026824

12) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390690/

13) https://www.ncbi.nlm.nih.gov/pubmed/9843377

14) https://www.ncbi.nlm.nih.gov/pubmed/12642378

The diagnosis is Li-Fraumeni syndrome, a multi-system cancer disorder due to mutations in TP53, the gene that codes for p53 tumor suppressor protein.¹

Pleiotropy is the well-established phenomenon of one gene causing multiple, unrelated phenotypic traits.²

Because mutations in TP53 can give rise to unrelated cancer phenotypes, the gene is highly pleiotropic.^{3, 4}

Variable expressivity refers to the manifestation of varying degrees of severity of a disease.⁵ TP53 is also cited heavily in the literature as causing variable expressivity,⁶ but the mere ability of the gene to cause unrelated phenotypes refers to pleiotropy, not variable expressivity. Variable expressivity would be the correct answer if the question asked why individuals in the family passed away at different ages or developed cancers of different aggressiveness; that is, “Why does one individual have it worse?” (variable expressivity) versus “Why did this gene cause different phenotypes?” (pleiotropy)

Mosaicism can be either somatic or germline. In somatic mosaicism, a % of one’s somatic (body) contain a different phenotype due to a post-fertilization mitotic error (e.g., 64% are one’s natural genotype; 36% are mutated). In germline mosaicism, 100% of an individual’s cells carry a disease (e.g., achondroplasia) despite the parents being unaffected because one of the parent’s (usually the father’s) primordial germ cells contains a mutation.⁷

Heteroplasmy refers to the presence of more than one type of mitochondrial DNA in the same individual. This means there is a non-uniformity of mitochondrial genes inherited (i.e., some cells contain one type of mitochondrial genome; other cells contain a different type, similar to mosaicism).⁸

Incomplete penetrance is when not all individuals who carry a disease genotype develop the phenotype (i.e., not all individuals with a disease actually express it).⁹

Bottom line: Pleiotropy is the ability of one gene to cause multiple, unrelated phenotypes. A USMLE-favorite example is TP53 causing Li-Fraumeni syndrome. In contrast, variable expressivity refers to the spectrum of severity of a disease, but not to the mere ability of the gene to manifest distinct phenotypes.

1) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135649/

2) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558540/

3) https://www.sciencedirect.com/science/article/pii/S0092867417309534

4) https://www.ncbi.nlm.nih.gov/pubmed/18639575

5) https://www.nature.com/scitable/topicpage/phenotype-variability-penetrance-and-expressivity-573/

6) https://books.google.co.jp/books?id=-97J-8Zh2hkC&pg

7) https://jmg.bmj.com/content/37/12/956

8) https://www.nature.com/articles/nrg3966

9) https://ghr.nlm.nih.gov/primer/inheritance/penetranceexpressivity

The diagnosis is Pompe disease (glycogen storage disease type II). It is caused by deficiency of alpha-1,4-glucosidase (lysosomal acid maltase).¹

You need to know that Pompe disease is the answer when you get a “heart problem” in a child with a glycogen storage disease. Cardiomyopathy is a characteristic feature.²

Glucose-6-phosphatase deficiency causes von Gierke disease (GSD type I). The presentation will often be an infant with lactic acidosis, hypoglycemia, hepatomegaly, and jaundice.³

Glucose-6-phosphate dehydrogenase deficiency is X-linked recessive and would not manifest in a girl. The characteristic presentation is hemolysis secondary to infection or oxidative drugs.⁴

Alpha-1,6-glucosidase deficiency causes Cori disease (GSD type III). Unlike Pompe disease, heart findings are far less common.⁵ 

Myophosphorylase (muscle glycogen phosphorylase) deficiency causes McArdle syndrome (GSD type V). Typical presentation is an adult with severe cramping and pain after exercise, with no lactic acidosis.⁶

Bottom line: You will get at least one glycogen storage disease question in some form on your USMLE. Memorize the basic presentations and enzyme deficiencies. (My post on glycogen storage diseases in much heavier detail is here. Open in a separate tab!)

1) https://www.cell.com/molecular-therapy-family/molecular-therapy/fulltext/S1525-0016(04)01468-6

2) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4241200/

3) https://www.ncbi.nlm.nih.gov/books/NBK534196/

4) https://www.aafp.org/afp/2005/1001/p1277.html

5) https://www.nature.com/articles/gim201069

6) https://jnnp.bmj.com/content/81/11/1182

 

In broad, heavily simplified terms:

Acetylated chromatin is known to increase the expression of genes through transcriptional activation¹; methylation is associated with repression / silencing of transcription.²

Likewise, deacetylation of histones causes chromatin condensation (silencing), while decondensation (activation) is caused by increased acetylation.³

So histone deacetylase inhibitors (DHAC) increase transcription.⁴

• Histone deacetylase → ↓ acetylation
• Therefore histone deacetylase inhibitor → ↑ acetylation
• ↑ acetylation → ↑ gene transcription

Bottom line: Acetylation = activation of genes. Methylation = silencing of genes. Once again, that’s heavily simplified, but for the USMLE that’s what they want.

1) https://mmbr.asm.org/content/64/2/435

2) https://www.nature.com/scitable/topicpage/the-role-of-methylation-in-gene-expression-1070/

3) https://www.ncbi.nlm.nih.gov/pubmed/20385088/

4) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5535906/

When DNA is transcribed to RNA in the nucleus by RNA polymerase II, the nascent RNA is called heteronuclear RNA (hnRNA).¹

This hnRNA does not float freely, but is instead immediately bound by ribonucleoproteins.¹

• hnRNA + ribonucleoproteins = hnRNPs

In order to become mRNA, three intranuclear modifications occur:¹

1. Addition of the 5′ 7-methylguanosine cap
2. Addition of 3′ Poly-A tail
3. Alternative splicing (i.e., splicing out of introns resulting in many combinations of intron-exon sequences)

The mRNA is then exported from the nucleus, where it is translated to protein. However it may also bind to P-bodies (Processing bodies), which carry various functions, but the main one is to sequester mRNA in a transiently repressed state, to be later released for translation.^{2, 3} In other words P-bodies act as a “docking site,” in order to “store” mRNA for future translation.

Bottom line: Addition of the 5′ 7-methylguanosine cap, addition of the 3′ Poly-A tail, and alternative splicing occur in the nucleus. These three mechanisms result in hnRNA → mRNA. Binding of mRNA to P-bodies occurs in the cytosol.

1) https://www.ncbi.nlm.nih.gov/books/NBK21563/

2) https://www.cell.com/trends/genetics/fulltext/S0168-9525(18)30090-8

3) https://www.sciencedirect.com/science/article/pii/B9780080450469020350

The ophthalmologist suspects von Hippel-Lindau syndrome (VHL), an autosomal dominant disorder on chromosome 3.¹

VHL is associated with cerebellar and retinal hemangioblastomas, renal cell carcinoma (often bilateral), and pheochromocytoma.²

This man’s eye finding is a retinal hemangioblastoma. His other fundoscopic findings have also been described in the literature.¹

Renal cell carcinoma (RCC in general, not just in VHL) is associated with erythropoietin (EPO) secretion, leading to polycythemia, and parathyroid hormone-related peptide (PTHrP) secretion, leading to hypercalcemia.³

Tangentially, the USMLE vignette may also say a male presenting with red urine and flank pain has hypercalcemia and polycythemia. What’s the diagnosis? → RCC.

A mass lesion capable of causing elevation of serum AFP levels refers to yolk sac tumor, hepatocellular carcinoma, hepadenoma, and mixed germ cell tumors.^{4, 5}

A mass lesion capable of causing Cushing syndrome and/or SIADH is small cell bronchogenic carcinoma.⁶

A mass lesion capable of causing myasthenia gravis is thymoma.⁷

Bottom line: VHL is an AD disorder on chromosome 3. The features are cerebellar and retinal hemangioblastomas, renal cell carcinoma (often bilateral), and pheochromocytoma. This disorder is exceedingly HY for the USMLE!

1) https://www.nature.com/articles/332268a0

2) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5541202/

3) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2219737/

4) https://www.ncbi.nlm.nih.gov/pubmed/8757478

5) https://www.ncbi.nlm.nih.gov/pubmed/1699854

6) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158371/

7) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155972/

This question is exceedingly HY for the USMLE.

This man has hereditary hemorrhagic telangiectasia (HHT; Osler-Weber-Rendu).

It is an autosomal dominant disorder characterized by multiple mucocutaneous telangiectasias, which represent small AV malformations. Patients typically present with epistaxis (nosebleeds) and GI bleeding leading to iron deficiency anemia.¹

It is estimated that 30-50% of those with HHT have pulmonary arteriovenous malformations (PAVM), and that 90% of individuals presenting with a PAVM have underlying HHT.^{2, 3, 4}

Arteriovenous malformations (not limited to pulmonary) are classically associated with high-output cardiac failure and bounding pulses.⁵

A pulse described as a “brisk upstroke with precipitous downstroke” refers to bounding pulses, and is a classic USMLE descriptor, often in aortic regurgitation (AR) questions. This vignette however is certainly PAVM, not AR.

Aortic stenosis is not classic for HHT. It presents with a slow-rising pulse (pulsus parvus et tardus), not a bounding pulse.⁶

Thoracic aortic dissection may be seen in various connective tissue disorders, such as Ehlers-Danlos syndrome, and is associated with blood pressure differing between the arms.⁷

Coarctation of the aorta is classically seen in Turner syndrome. It presents with blood pressure much greater in the brachial artery (arm) compared to the femoral artery.⁸

Bottom line: Hereditary hemorrhagic telangiectasia is an AD disorder characterized by epistaxis, mucucutaneous telangiectasias, and GI bleeding leading to iron deficiency anemia. 30-50% of patients will go on to develop pulmonary arteriovenous malformations, which may result in high-output cardiac failure.

1) https://www.ncbi.nlm.nih.gov/books/NBK482361/

2) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3835466/

3) https://www.ncbi.nlm.nih.gov/pubmed/14742303/

4) https://www.ncbi.nlm.nih.gov/pubmed/20154077/

5) https://www.ncbi.nlm.nih.gov/pubmed/21223485

6) https://www.ncbi.nlm.nih.gov/pubmed/28679515

7) https://www.sciencedirect.com/science/article/pii/S2211558712000556

8) https://www.mayoclinic.org/diseases-conditions/coarctation-of-the-aorta/symptoms-causes/syc-20352529

Familial hyperchylomicronemia is an AR disorder with a mean onset of diagnosis at age 24. It is characterized by high serum TGAs and LDL.^{1, 2}

It is caused by deficiency of either lipoprotein lipase (LPL) or apolipoprotein C-II.³

Apolipoprotein C-II is a cofactor for LDL.⁴

LPL promotes the uptake of fatty acids from chylomicrons by peripheral tissues. The resultant chylomicron remnants then return to the liver and require apolipoprotein E for hepatic uptake. The particles are then released by the liver into the circulation as VLDL, which return to peripheral tissues and unload fatty acids. Uptake of the fatty acids into tissues requires apolipoprotein C-II and LPL. The unloading of fatty acids will continue through cycles until the particles become LDL, which are proportionally less TGA by mass compared to VLDL.⁵

Familial hypercholesterolemia is AD and due to a loss-of-function mutation in the LDL receptor.⁶

Familial hypertriglyceridemia is AD and due to increased hepatic production of VLDL.⁷

Hormone-sensitive lipase is necessary for the lipolysis and release of TGAs into the circulation from adipocytes.⁸

Bottom line: Know the mechanisms of the above three familial dyslipidemias for the USMLE.

1) https://www.sciencedirect.com/science/article/pii/S1933287418302423

2) https://www.ncbi.nlm.nih.gov/pubmed/30183397

3) https://www.ncbi.nlm.nih.gov/pubmed/1479292

4) https://www.ncbi.nlm.nih.gov/pubmed/2307668

5) https://link.springer.com/article/10.1007%2Fs00109-002-0384-9

6) https://www.ncbi.nlm.nih.gov/pubmed/17380167

7) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839776/

8) https://diabetes.diabetesjournals.org/content/51/12/3368

MCAD is an enzyme required for fatty acid beta-oxidation.¹ Deficiency causes:

• Hypoketotic hypoglycemia¹
• Increased serum medium-chain acylcarnitines (notably C8-acylcarnitines)¹
• Increased urinary medium-chain dicarboxylic acids¹

Medium-chain fatty acids are 6-12 carbons in length.^{2, 3} Long-chain fatty acids are 12-22 carbons in length^{2, 3}, and are usually 16-18 carbons long.⁴ Very long-chain fatty acids are >22 carbons in length.⁵

Based on the length of the acylcarnitines and dicarboxylic acids seen in the patient’s serum and urine, respectively, she has MCAD, not LCAD or VLCAD deficiency.

Carnitine deficiency is differentiated from MCAD, LCAD, and VLCAD deficiencies in that free serum carnitine is decreased.¹

Hypoglycemia is seen because tissues must utilize more glucose in order to compensate for lack of energy derived from fatty acid metabolism.¹ In addition, decreased acetyl-CoA production decreases the positive allosteric regulation of pyruvate carboxylase, thereby contributing to decreased effectiveness of glucose production.⁶

Hypoketosis (↓ ketones) is seen because ↓ beta-oxidation of fatty acids means ↓ acetyl-CoA production in the catabolic state, and acetyl-CoA are the starting point for ketone synthesis.⁷

Bottom line: MCAD, LCAD, VLCAD, and carnitine deficiencies are occasionally tested on USMLE Step 1. Hypoketotic hypoglycemia is characteristic of all three. In the latter, serum free carnitine is decreased; it is normal in MCAD, LCAD, VLCAD deficiencies. The latter three conditions are differentiated based on the serum fatty acylcarnitine and urine dicarboxylic acid length.

1) https://www.ncbi.nlm.nih.gov/books/NBK1424/

2) https://www.sciencedirect.com/science/article/pii/B9781416036616000328

3) https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/medium-chain-fatty-acids

4) https://www.sciencedirect.com/topics/medicine-and-dentistry/long-chain-fatty-acid

5) https://www.ncbi.nlm.nih.gov/pubmed/22984005

6) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859305/

7) https://www.sciencedirect.com/science/article/pii/B012227055X006635

The diagnosis is N-acetylglutamate synthase deficiency (NAGSD).

N-acetylglutamate is a positive allosteric regulator of carbamoyl phosphate synthetase I, the rate-limiting enzyme of the urea cycle.^{1, 2}

Hyperammonemia is the principal finding in NAGSD, in addition to increased alanine, normal glutamate, decreased citrulline, and decreased arginine.¹

In order to answer this question correctly, you wouldn’t have needed to have memorized these findings per se, but more that if you know the general functions of the enzymes listed, you could infer that NAGSD is the only reasonable answer.

UMPS is an enzyme involved in pyrimidine synthesis. Deficiency causes orotic aciduria, a condition characterized by megaloblastic anemia and increased serum orotic acid.³

Argininosuccinate synthetase is a urea cycle enzyme (as you can see in the diagram above). Deficiency in this case cannot be correct because serum citrulline would be increased, not decreased. In fact, deficiency of this enzyme causes citrullinemia type I.⁴ (No you do not need to know that for the USMLE)

Carbamoyl phosphate synthetase I, not II, is the rate-limiting enzyme of the urea cycle. Deficiency of CPS I, not CPS II, would cause findings akin to NAGSD. CPS II is the first enzyme in pyrimidine biosynthesis.⁵

Bottom line: N-acetylglutamate is a positive allosteric regulator of carbamoyl phosphate synthetase I, the rate-limiting enzyme of the urea cycle. Deficiency of N-acetylglutamate synthase causes hyperammonemia and decreased urea cycle amino acids (citrulline and arginine).

1) https://www.nature.com/articles/s41598-018-33457-0

2) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176164/

3) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393157/

4) https://www.ncbi.nlm.nih.gov/books/NBK1458/

5) https://link.springer.com/chapter/10.1007/978-1-4615-5381-6_46

The diagnosis is scombroid, a pseudoallergenic poisoning caused by the consumption of contaminated fish belonging to the Scombridae family (i.e., tuna, mackerel, swordfish, etc.). It is caused by increased histamine content within the decaying fish secondary to bacterial production of histidine decarboxylase.¹

• Histidine (via histidine decarboxylase) → histamine

Scombroid is often misdiagnosed as a seafood allergy because symptomatology is similar – i.e., patients may develop severe dyspnea with facial flushing, a diffuse maculopapular body rash, urticaria, and abdominal cramping.²

Ciguatera is caused by ciguatera toxin, which activates sodium channels in neurons and causes temperature dysesthesia (i.e., “hot feels cold; cold feels hot”). Ciguatera is acquired by eating meaty reef fish, such as mackerel, barracuda, kingfish, moray eel, etc.³

Tetrodotoxin inhibits sodium channels and causes paralysis. It is acquired by eating pufferfish.⁴

You do not need to know Haff disease or Ichthyoallyeinotoxism for the USMLE. Haff disease presents as rhabdomyolysis after eating fish.⁵ Ichthyoallyeinotoxism produces hallucinations similar to LSD.⁶

It should also be noted that shellfish allergy may present similarly to scombroid. Because scombroid does not result from eating shellfish, if the question stem mentions shellfish consumption, make sure you choose shellfish allergy, not scombroid. Just because you might learn of something weird and cool called scombroid, don’t get all trigger-happy and erroneously choose it if the vignette mentions shellfish.

Bottom line: Know scombroid, ciguatera, and tetrodotoxin for the USMLE. Scombroid is often misdiagnosed as seafood allergy. Ciguatera presents as “hot feels cold; cold feels hot.” Tetrodotoxin presents as paralysis. Scombroid does not result from eating shellfish; don’t get all Texan trigger-happy and choose scombroid if the vignette mentions shellfish.

1) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273511/

2) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3314039/

3) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579736/

4) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626696/

5) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640861/

6) https://www.tandfonline.com/doi/abs/10.1080/15563650

Intramuscular epinephrine is used to treat anaphylaxis.¹

The final step of the biosynthesis requires a methylation of norepinephrine.

You might say, “Who the fuck cares.” It’s because epinephrine agonizes β2-receptors, whereas norepinephrine does not.² The difference in binding is due to the methyl group on epinephrine.³ It is the ability to agonize β2 that causes bronchiolar dilatation and alleviation of the respiratory distress of anaphylaxis.⁴

Norepinephrine binds: α1, α2, β1²

Epinephrine binds: α1, α2, β1, β2² 

Bottom line: Epinephrine has a methyl group. Norepinephrine does not. Epinephrine binds α1, α2, β1, and β2. Norepinephrine only binds α1, α2, and β1. This difference in affinity is explained by the methyl group. Wild and crazy.

1) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4129903/

2) https://www.ncbi.nlm.nih.gov/books/NBK534230/

3) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC365690/

4) https://books.google.co.jp/books?id=0jGB8UHyRG0C&pg=PA244&lpg

The child has maple syrup urine disease, which is caused by a deficiency of branched-chain ketoacid dehydrogenase. It results in an inability to metabolize the amino acids leucine, isoleucine, and valine.¹

It presents as poor feeding, vomiting, and generalized convulsions in a neonate who has a notable odor of burnt sugar coming from his urine and cerumen (ear wax).^{2, 3}

Treatment requires a special diet and avoidance of dietary leucine, isoleucine, and valine.⁴

The four thiamine-(vitamin B1) dependent enzymes are:

• Transketolase⁵
• Alpha-ketoglutarate dehydrogenase⁵
• Pyruvate dehydrogenase⁵
• Branched-chain ketoacid dehydrogenase⁶

Therefore, branched-chain ketoacid dehydrogenase shares thiamine as a cofactor with transketolase.

Pyruvate carboxylase requires biotin (B7) as a cofactor, not thiamine.⁷

Glutamic acid decarboxylase requires pyridoxine (B6) as a cofactor.⁸

Succinate dehydrogenase in the TCA cycle requires riboflavin (B2) as a cofactor.⁹

Methylmalonyl-CoA mutase requires cyanocobalamin (B12) as a cofactor.¹⁰

Bottom line: Maple syrup urine disease is caused by a deficiency of branched-chain ketoacid dehydrogenase, resulting in an inability to metabolize the amino acids leucine, isoleucine, and valine. Know the four thiamine-dependent enzymes for the USMLE. 

1) https://www.ncbi.nlm.nih.gov/books/NBK1319/

2) https://www.ncbi.nlm.nih.gov/pubmed/7904856

3) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5593394/

4) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2019098/

5) https://www.ncbi.nlm.nih.gov/pubmed/8279670

6) http://www.jbc.org/content/282/16/11904.full

7) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859305/

8) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4954698/

9) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5447943/

10) https://www.ncbi.nlm.nih.gov/pubmed/22661206

The diagnosis is alkaptonuria, an autosomal recessive disease caused by deficiency of homogentisic acid oxidase (homogentisate oxidase), resulting in impaired metabolism of the amino acid tyrosine.¹

Buildup of homogentisic acid leads to deposition in collagenous tissues, such as the pinna of the ear, sclerae, and fingers, causing them to take on a grey, black, or blue discoloration referred to as ochronosis.^{1, 2}

Ochronotic arthropathy, which literally means “dark-colored joint pathology,” presents in 50% of patients by age 40 and causes joint deterioration, notably spondyloarthropathy.^{1, 2}

A classic finding in USMLE vignettes is darkening of the urine upon standing, but this may also occur with semen.^{1, 3}

Bottom line: Alkaptonuria is a HY disorder on the USMLE. It is due to deficiency of homogentisic acid oxidase (homogentisate oxidase), resulting in impaired metabolism of the amino acid tyrosine. Ochronosis, ochronotic arthropathy, and darkening of the urine upon standing are characteristic findings.

1) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978898/

2) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3019075/

3) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155960/