USMLE Biochemistry Syllabus

Name the three tRNA-binding sites of the ribosome and their roles.

A (aminoacyl) accepts incoming charged tRNA, P (peptidyl) holds the growing chain, E (exit) releases the deacylated tRNA.

What are the eukaryotic and prokaryotic ribosomal subunit compositions?

Eukaryotic: 40S + 60S $\to$ 80S. Prokaryotic: 30S + 50S $\to$ 70S (mnemonic: even = eukaryotes).

Which energy sources power aminoacyl-tRNA charging and translocation during translation?

Charging by aminoacyl-tRNA synthetase uses ATP $\to$ AMP + $\ce{PP_i}$; ribosomal translocation (EF-2/EF-G) uses GTP hydrolysis.

State Mendel's law of segregation.

The two alleles of a gene separate during gamete formation, so each gamete carries only one allele of the pair.

State Mendel's law of independent assortment.

Alleles of different genes assort independently into gametes (applies to genes on different chromosomes or far apart on the same chromosome).

For a monohybrid cross $Aa \times Aa$, give the genotypic and phenotypic ratios.

Genotypic ratio $1\,AA : 2\,Aa : 1\,aa$; phenotypic ratio $3\,\text{dominant} : 1\,\text{recessive}$.

Give the Hardy-Weinberg equations for allele and genotype frequencies.

$p + q = 1$ and $p^{2} + 2pq + q^{2} = 1$, where $p^{2}$ = homozygous dominant, $2pq$ = heterozygous, $q^{2}$ = homozygous recessive.

How does an X-linked recessive inheritance pattern typically present in a pedigree?

Predominantly affected males, no male-to-male transmission, carrier mothers pass to sons; daughters of affected males are obligate carriers.

Contrast autosomal dominant with autosomal recessive inheritance regarding vertical transmission.

Autosomal dominant: often affected in every generation (vertical), both sexes equally, ~50% offspring risk. Autosomal recessive: often skips generations, requires two carriers, ~25% offspring risk.

Define incomplete dominance versus codominance.

Incomplete dominance: heterozygote shows a blended/intermediate phenotype (e.g., pink flower). Codominance: both alleles are fully and simultaneously expressed (e.g., AB blood group).

What is genomic imprinting, and name the two classic imprinting disorders at 15q11-13.

Differential gene expression depending on parent of origin. Prader-Willi (loss of paternal allele) and Angelman (loss of maternal allele).

Distinguish a transition from a transversion mutation.

Transition: purine$\to$purine or pyrimidine$\to$pyrimidine substitution. Transversion: purine$\leftrightarrow$pyrimidine substitution.

Compare silent, missense, and nonsense point mutations by their effect on protein.

Silent: same amino acid (often wobble position). Missense: different amino acid. Nonsense: creates a premature stop codon, truncating the protein.

What is a frameshift mutation and what causes it?

An insertion or deletion of a number of nucleotides not divisible by 3, shifting the reading frame and usually producing a nonfunctional/truncated protein.

What molecular mechanism underlies trinucleotide repeat expansion diseases, and give the Huntington repeat.

Unstable expansion of tandem repeats causing anticipation (worsening/earlier onset over generations). Huntington disease expands CAG repeats.

What type of mutation causes sickle cell anemia, and what is the amino acid change?

A missense point mutation ($\ce{A -> T}$) in the $\beta$-globin gene, replacing glutamate with valine at position 6 (Glu6Val).

Define a loss-of-function versus a gain-of-function mutation.

Loss-of-function reduces or abolishes a gene product's activity (often recessive). Gain-of-function confers a new or enhanced activity (often dominant).

Distinguish germline from somatic mutations in terms of heritability.

Germline mutations occur in gametes and are heritable/present in all cells; somatic mutations arise in body cells and are not passed to offspring.

What is the fundamental principle of gene therapy?

Introducing, correcting, or silencing genetic material in a patient's cells to treat disease, either by adding a functional gene copy, editing the defect, or knocking down a harmful transcript.

Compare adeno-associated virus (AAV) and lentivirus as gene therapy vectors.

AAV: non-integrating (mostly episomal), low immunogenicity, small cargo (~$4.7$ kb), long expression in non-dividing cells. Lentivirus: integrates into the genome, larger cargo, stable expression in dividing cells but insertional mutagenesis risk.

How does the CRISPR-Cas9 system achieve targeted gene editing?

A guide RNA directs Cas9 nuclease to a complementary DNA sequence adjacent to a PAM, where Cas9 makes a double-strand break repaired by NHEJ (knockout) or HDR (precise correction).

What is the mechanism of RNA interference (siRNA/antisense) therapy?

Small interfering RNA or antisense oligonucleotides bind complementary mRNA, promoting its degradation or blocking translation to reduce production of a target protein.

Contrast in vivo and ex vivo gene therapy approaches.

In vivo: vector delivered directly into the patient's body. Ex vivo: patient's cells are removed, genetically modified in culture, then reinfused (e.g., CAR-T, hematopoietic stem cell therapy).

What is the net ATP yield of glycolysis per glucose, and where does it occur?

Net $\mathbf{2}$ ATP (4 produced $-$ 2 consumed) plus 2 NADH; it occurs in the cytoplasm. $$\text{glucose} + 2\,\text{ADP} + 2\,\ce{P_i} + 2\,\text{NAD}^{+} \to 2\,\text{pyruvate} + 2\,\text{ATP} + 2\,\text{NADH}$$

Which is the rate-limiting (committed) enzyme of glycolysis and its key allosteric regulators?

Phosphofructokinase-1 (PFK-1). Activated by AMP and fructose-2,6-bisphosphate; inhibited by ATP and citrate.

How much ATP is generated by complete aerobic oxidation of one glucose molecule?

Approximately $30\text{-}32$ ATP total (glycolysis, pyruvate dehydrogenase, TCA cycle, and oxidative phosphorylation combined).

What is the primary role of the pentose phosphate pathway, and which enzyme is rate-limiting?

It generates NADPH (for reductive biosynthesis and glutathione reduction) and ribose-5-phosphate for nucleotides. Rate-limiting enzyme: glucose-6-phosphate dehydrogenase (G6PD).

What are the substrate, key enzyme, and rate-limiting step of fatty acid $\beta$-oxidation?

Acyl-CoA is oxidized in the mitochondrial matrix; the rate-limiting entry step is carnitine transport via carnitine palmitoyltransferase I (CPT-1), which is inhibited by malonyl-CoA.

Which three ketone bodies are produced in the liver, and which cannot be used as fuel?

Acetoacetate and $\beta$-hydroxybutyrate are used as fuel by peripheral tissues; acetone is a volatile byproduct that is exhaled and not used for energy.

Distinguish glucogenic from ketogenic amino acids, naming the two purely ketogenic ones.

Glucogenic amino acids yield gluconeogenesis intermediates; ketogenic yield acetyl-CoA/acetoacetate. The only purely ketogenic amino acids are leucine and lysine (mnemonic: onLy Leucine and Lysine).

What is the fate of the amino group during amino acid catabolism, and by what cycle is it excreted?

The amino group is transferred (transamination) then released as ammonia and detoxified to urea via the urea cycle; the rate-limiting enzyme is carbamoyl phosphate synthetase I in the mitochondria.