Transmission of genetic information from the gene to the protein

Remember the rings with "PURe As Gold" (purines = A, G, double ring) vs. the pyrimidines C, U, T (single ring) — "CUT the py(e)". A nucleoside is base + sugar; a nucleotide adds the phosphate(s). Nucleotides do double duty beyond heredity: ATP/GTP carry energy, and NAD⁺/FAD/coenzyme A are nucleotide-derived coenzymes.

Complementary bases pair through hydrogen bonds — A–T (2 bonds) and G–C (3 bonds) — always a purine with a pyrimidine, which keeps the helix a constant width. The strands run antiparallel, a fact that drives the whole logic of replication and transcription (polymerases only build 5′→3′). Chargaff's rules: in any double-stranded DNA, %A = %T and %G = %C. The backbone is on the outside; the stacked base pairs are inside, with major and minor grooves where proteins read the sequence.

Because G–C pairs have three hydrogen bonds to A–T's two, GC-rich sequences need more energy to separate, so they have a higher Tm. This is the basis of PCR (heat to denature, cool to anneal primers) and of probe hybridization.

In RNA, the 2′-hydroxyl sits one carbon away from the phosphodiester linkage and can act as an internal nucleophile, attacking the phosphate to break the backbone — so RNA is base-labile and hydrolyzes far more readily than DNA, especially at high pH. DNA's sugar is deoxyribose precisely because removing that 2′-OH eliminates the self-cleavage pathway, giving the genome the chemical durability it needs to persist for the life of the cell. This is the structure-explains-function payoff of the deoxyribose-vs-ribose distinction: messenger RNA is meant to be transcribed, translated, and degraded (turnover lets the cell adjust protein output quickly), whereas the DNA archive must not turn over. The trade-off also explains why labs handle RNA with extra care (ubiquitous RNases, cold, RNase-free reagents) but DNA is comparatively rugged.

In order: helicase breaks the H-bonds to open the fork; single-strand binding proteins keep it open; topoisomerase/DNA gyrase cuts and reseals ahead of the fork to relieve the torsional strain of unwinding. Primase synthesizes a short RNA primer that gives DNA polymerase a 3′-OH to build on. In prokaryotes, DNA polymerase III is the main builder; DNA polymerase I removes the RNA primers and replaces them with DNA; DNA ligase joins the fragments.

Toward the fork, the leading strand is synthesized continuously in the same direction the fork opens. The lagging strand runs the "wrong way," so it's made in short Okazaki fragments, each needing its own primer, synthesized away from the fork and then stitched together by ligase. This is the single most-tested mechanical detail in replication.

Proofreading (3′→5′ exonuclease) removes a mis-incorporated base immediately, dropping the error rate enormously; mismatches that slip past are caught later by repair (next topic). Because the lagging strand can't be fully primed at the very end, linear chromosomes lose a little length each round — telomeres (repetitive caps) absorb the loss, and telomerase (active in germ cells, stem cells, and many cancers) rebuilds them.

A silent mutation is buffered by the genetic code's redundancy. A missense swaps one amino acid (sickle-cell is the classic). A nonsense mutation introduces a premature stop codon, truncating the protein. Insertions or deletions that aren't multiples of three cause a frameshift, garbling every codon downstream — usually far more damaging than a point mutation.

Three RNAs run translation: messenger RNA (mRNA) is the transcript that gets read; transfer RNA (tRNA) is the adaptor that matches a codon (via its anticodon) to the correct amino acid; ribosomal RNA (rRNA) is the structural and catalytic core of the ribosome (a ribozyme). Eukaryotes have three RNA polymerases (I, II, III) for rRNA, mRNA, and tRNA respectively; prokaryotes have one.

Three modifications turn the primary transcript (pre-mRNA) into mature mRNA: a 5′ methylguanosine cap (protects the message and aids ribosome binding), a 3′ poly-A tail (stability and export), and splicing — the spliceosome (snRNPs) removes introns (intervening, non-coding) and joins exons (expressed). Alternative splicing — including different exon combinations from the same transcript — is a major reason humans make far more proteins than they have genes. Prokaryotes do none of this (no nucleus; transcription and translation are coupled).

64 codons encode 20 amino acids plus stop signals, so the code is degenerate/redundant — often the third base can vary (wobble), which is why many point mutations are silent. The start codon AUG sets the reading frame and codes for methionine; UAA, UAG, UGA are stops (no amino acid). The code is nearly universal across life, which is what makes recombinant protein expression possible.

Accuracy of translation depends on two recognition steps: the aminoacyl-tRNA synthetase attaching the right amino acid to the right tRNA (charging, ATP-dependent), and the anticodon–codon pairing at the ribosome. There's one synthetase family per amino acid, and they proofread — a mischarged tRNA would insert the wrong residue regardless of the codon.

The primary sequence is only the start. An N-terminal signal peptide (signal sequence) directs a nascent protein to the rough ER for secretion or membrane insertion and is cleaved off once the protein arrives. Reversible chemical modifications tune function: phosphorylation (a regulatory phosphate added by kinases) switches activity on or off, glycosylation (adding sugars in the ER/Golgi) marks proteins for the cell surface or secretion, and lipidation (attaching a lipid group) anchors proteins to membranes. Proteolytic activation is an irreversible cleavage that switches an inactive zymogen on (e.g., trypsinogen → trypsin). For disposal, ubiquitination tags a protein with ubiquitin, marking it for degradation and recycling by the proteasome.

Each ribosome has a small subunit (decodes the mRNA) and a large subunit (forms peptide bonds via its rRNA ribozyme). In prokaryotes these are 30S + 50S → 70S; in eukaryotes they are 40S + 60S → 80S (the cytosolic ribosome — mitochondria carry their own 70S-like ribosomes, a clue to their bacterial origin). The size difference is what makes ribosome-targeting antibiotics selective: drugs like aminoglycosides and tetracyclines bind the bacterial 30S and spare the human 80S.

An operon = promoter + operator + structural genes, with a repressor protein that binds the operator to block transcription. lac (inducible): normally the repressor is bound (off); allolactose (from lactose) inactivates the repressor, turning it on — and it's also positively controlled: low glucose → high cAMP → CAP binds and boosts transcription, so maximal expression needs lactose present and glucose low. trp (repressible): normally on; when tryptophan is plentiful it acts as a corepressor, activating the repressor to shut synthesis off. The pattern: catabolic pathways tend to be inducible, anabolic ones repressible.

DNA wraps around histones into nucleosomes; tightly packed heterochromatin is silent, loosely packed euchromatin is active. Histone acetylation loosens packing (→ more transcription); DNA methylation (at CpG islands) tightens it (→ silencing). Transcription factors bind promoters and distant enhancers (or silencers) to recruit or block RNA polymerase. These epigenetic modifications are heritable through cell division without altering the DNA sequence, and explain how identical genomes yield different cell types.

Each cycle: ~95 °C denatures the strands, cooling anneals two primers flanking the target, and Taq polymerase (from a thermophile, so it survives the heat steps) extends from the primers. Because every cycle doubles the product, amplification is exponential (2ⁿ). PCR underlies diagnostics, forensics, and qPCR for quantifying expression.

Restriction endonucleases cut at palindromic recognition sites, and matching sticky ends plus ligase let you splice DNA into plasmid vectors (recombinant DNA / cloning). Gel electrophoresis drives negatively charged DNA toward the anode, separating fragments by size (smaller travel farther). The blots follow one rule — "Southern = DNA, Northern = RNA (RNA, by the second letter), Western = protein." Sanger (chain-termination) sequencing reads a sequence using dideoxynucleotides; CRISPR-Cas9 uses a guide RNA to target and cut a chosen sequence for editing.

In vitro ("in glass") strips a process down to its parts — a purified enzyme in a tube, cells in a dish — so you can control every variable, but you lose the surrounding physiology. In vivo keeps the process embedded in a living system (whole animal, intact tissue), so it's realistic but full of confounders. The MCAT's recurring move is the transfer question: a clean in vitro result (e.g., a drug inhibits an enzyme in a tube) may not hold in vivo, where absorption, metabolism, compartmentalization, and feedback all intervene.