MCAT

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Dna

Rna

Replication copies the genome

Transcription by RNA polymerase

Translation on ribosomes

Transcription

Transcription synthesizes RNA from a DNA template. RNA polymerase forms phosphodiester bonds in the 5′ to 3′ direction using ribonucleoside triphosphates. Prokaryotes use a single RNA polymerase; its sigma factor recognizes promoter sequences, including the −10 box (TATAAT, Pribnow box) and the −35 box. Transcription ends at intrinsic terminators (a hairpin followed by a U-rich sequence) or by rho-dependent termination.

Polymerase	Transcribes
RNApolymeraseI	rRNAgenes(except5S)
RNApolymeraseII	mRNAandsomesmallRNAs
RNApolymeraseIII	tRNA 5SrRNA andothersmallRNAs , ,

Eukaryotic promoters contain core elements (TATA box, initiator element, downstream core promoter element) and regulatory elements (enhancers, silencers). The general transcription factors TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH assemble at the promoter to recruit RNA polymerase II.

Splicing involves two transesterification reactions. The 2′-OH of a branch-point adenosine attacks the 5′ splice site, forming a lariat intermediate; the 3′-OH of the upstream exon then attacks the 3′ splice site, joining the exons and releasing the lariat. Alternative splicing produces several mRNA variants from one gene by using different combinations of exons, expanding protein diversity without enlarging the genome.

Translation

Translation builds polypeptides from mRNA using ribosomes and tRNAs. The genetic code is read in triplet codons: 64 codons encode 20 amino acids plus stop signals. The code is degenerate (several codons can encode one amino acid), unambiguous (each codon specifies one amino acid), and nearly universal. The start codon AUG encodes methionine; the stop codons are UAA, UAG, and UGA. The wobble hypothesis explains how fewer than 61 tRNAs can read all sense codons through flexible pairing at the third codon position.

Each tRNA has an anticodon that pairs with the mRNA codon and an acceptor stem that carries the amino acid. Aminoacyl-tRNA synthetases charge tRNAs with the correct amino acid in a two-step reaction. Prokaryotic ribosomes are 70S (30S + 50S); eukaryotic ribosomes are 80S (40S + 60S). The small subunit holds the decoding center, and the large subunit contains the peptidyl transferase center.

Stage	KeyEvents
Initiation	Prokaryotes: the 30S subunit binds the Shine-Dalgarno sequence upstream of the start codon then the initiator ,
	tRNA (N -formylmethionine) and the 50S subunit join Eukaryotes: the 40S subunit with initiator tRNA .
	(methionine)bindsthe5′capandscansforthestartcodon
Elongation	Aminoacyl -tRNA enters the A site (EF-Tu in prokaryotes eEF1A in eukaryotes); peptidyl transferase forms the ,
	peptide bond; translocation (EF-G eEF2) shifts tRNAs from A to P and P to E sites ,
Termination	A stop codon enters the A site; release factors trigger hydrolysis of the peptidyl -tRNA bond releasing the , polypeptide

Post-translational modifications include proteolytic cleavage, glycosylation, phosphorylation, lipidation, and disulfide bond formation. Signal sequences target proteins to their destinations.

Gene Regulation

Without lactose, the lac repressor binds the operator and

Tryptophan acts as a corepressor: it binds the trp repressor so

blocks transcription. Allolactose binds the repressor, releasing

the repressor can bind the operator when tryptophan is

the operator. Positive control: low glucose raises cAMP, which

abundant. Attenuation adds control through premature

binds CAP to enhance transcription.

termination.

Eukaryotic regulation operates at many levels. Histone acetylation generally increases transcription by loosening chromatin; histone methylation can activate or repress depending on the residue; DNA methylation (especially at CpG islands) typically represses. Transcription factors bind enhancers, silencers, and response elements; activators recruit coactivators and the transcription machinery, while repressors recruit corepressors or block activators. After transcription, microRNAs and small interfering RNAs bind complementary mRNA to cause degradation or translational repression.

Epigenetics refers to heritable changes in gene expression without changes in DNA sequence, through DNA methylation, histone modification, and chromatin remodeling. These marks can pass through cell division and sometimes across generations.

Recombinant DNA Technology

Technique	WhatItDoes
Restrictionenzymes	CutDNAatspecificrecognitionsequences;typeIIenzymescutatdefinedpositionsandmany
	leavestickyendsthateaseligation
DNAcloning	InsertsforeignDNAintoavector(plasmid bacteriophage orartificialchromosome)withanorigin , ,
	ofreplication selectablemarker andmultiplecloningsite , ,
PCR	Amplifiesasequenceexponentiallythroughcyclesofdenaturation primerannealing and , ,
	extension;ncyclesyield2ncopies
Gelelectrophoresis	Separatesfragmentsbysize;smallerfragmentsmigratefaster
Blotting	Southern(DNA) Northern(RNA) Western(protein) , ,
Sangersequencing	Dideoxynucleotides terminate chains at specific bases; next-generation methods sequence at high
	throughput
CRISPR-Cas9	Guide RNA directs Cas9 to cut a target sequence; repair by error-prone nonhomologous end
	joining causes insertions or deletions while homology-directed repair makes precise edits when a ,
	templateissupplied