Molecular Biology: DNA Structure, Replication, Gene Expression, and Regulation

Flashcards providing comprehensive vocabulary coverage of nucleic acid biochemistry, DNA replication, transcription, RNA processing, translation, and prokaryotic/eukaryotic gene regulation based on the lecture slides.

Nucleotide

A molecular subunit of nucleic acids consisting of one, two, or three phosphate groups, a five-carbon sugar (ribose or deoxyribose), and a single- or double-ring nitrogenous base.

Nucleoside

The portion of a nucleotide that contains only the five-carbon sugar and the nitrogenous base, lacking any phosphate groups.

Sugar-Phosphate Backbone

The structural chain of alternating sugars and negatively charged phosphate groups in a nucleic acid, possessing a directional polarity defined by unlinked $5'$ and $3'$ carbons.

Hershey-Chase Experiment

A 1952 experiment by Alfred Hershey and Martha Chase that used bacteriophage T2 labeled with $^{35}\text{S}$ (protein) and $^{32}\text{P}$ (DNA) to demonstrate that DNA, not protein, enters bacterial cells and serves as the genetic material.

Chargaff's Rule

The biochemical principle established by Erwin Chargaff showing that in cellular DNA, the ratio of adenine equals thymine ($A = T$) and guanine equals cytosine ($G = C$), and that base composition varies across species but is identical within tissues of the same species.

Photo 51

The historic X-ray diffraction photograph of DNA taken by Rosalind Franklin that provided critical evidence of DNA's helical structure, dimensions, and regular repeating units.

Antiparallel Strands

The structural arrangement of the two complementary polynucleotide chains in double-stranded DNA running side-by-side in opposite directions ($5'\rightarrow 3'$ and $3'\rightarrow 5'$).

Major and Minor Grooves

The two spiral indentations of unequal size along the DNA double helix where the outer edges of nitrogenous base pairs remain chemically exposed for hydrogen bonding and protein interactions.

Stacking Interactions

Non-covalent stabilizing forces between adjacent flat base pairs along a polynucleotide strand in a double helix, comprising van der Waals, electrostatic, and hydrophobic interactions.

Ribozyme

An RNA molecule capable of functioning as an enzyme to catalyze specific biochemical reactions, such as peptide bond formation in ribosomes.

Hairpin (Stem-Loop)

A common secondary structure formed in single-stranded RNA when complementary bases on the same strand fold back and base-pair into an antiparallel double-stranded stem capped by an unpaired loop.

Semiconservative Replication

The mode of DNA replication where the two parental strands separate and each acts as a template for a new strand, yielding daughter duplexes composed of one conserved parental strand and one newly synthesized strand.

Meselson-Stahl Experiment

A 1958 experiment by Matthew Meselson and Frank Stahl that grew E. coli in heavy $^{15}\text{N}$ medium, transferred them to light $^{14}\text{N}$, and separated DNA by density gradient centrifugation, proving semiconservative replication.

Origin of Replication (ori)

A specific nucleotide sequence in a chromosome where replication complexes bind and DNA replication is initiated.

Replication Bubble

The unwound open region of DNA formed at an origin of replication from which two active replication forks proceed bidirectionally.

Type II Topoisomerase

An enzyme that relieves twisting forces and torsional stress ahead of the replication fork by cleaving both strands of DNA simultaneously, passing a second duplex through the break, and resealing the cut.

Single-Strand DNA-Binding Proteins (SSBPs)

Proteins that attach to exposed single-stranded template DNA behind the helicase to stabilize the strands and prevent them from snapping back together or reannealing.

Primase

A specialized RNA polymerase that synthesizes a short RNA primer without needing a preexisting $3'\text{-OH}$ group, enabling DNA polymerase to begin synthesizing DNA.

Leading Strand

The continuously synthesized DNA strand that extends into the advancing replication fork in the $5'\rightarrow 3'$ direction.

Lagging Strand

The discontinuously synthesized DNA strand that is replicated away from the advancing replication fork as a series of short segments.

Okazaki Fragments

Short stretches of newly synthesized DNA produced discontinuously on the lagging strand template during DNA replication.

DNA Polymerase III

The primary bacterial enzyme responsible for elongating both the leading and lagging DNA strands in the $5'\rightarrow 3'$ direction during chromosome replication.

DNA Polymerase I

A bacterial repair and replication enzyme that uses $5'\rightarrow 3'$ exonuclease activity to degrade RNA primers and simultaneously replaces them with deoxyribonucleotides via its polymerase activity.

DNA Ligase

An enzyme that seals breaks in the phosphodiester backbone by joining the adjacent $3'\text{-OH}$ and $5'\text{-phosphate}$ ends of DNA fragments.

Replisome

A large multi-enzyme macromolecular complex containing DNA polymerases, helicase, primase, and other replication proteins that coordinates synthesis at a replication fork.

Telomeres

Repetitive, non-coding nucleotide sequences (such as $\text{TTAGGG}$ in humans) found at the ends of linear eukaryotic chromosomes that safeguard genomic DNA against shortening during replication.

Telomerase

A ribonucleoprotein reverse transcriptase that maintains linear chromosome ends by synthesizing repetitive DNA onto the $3'$ overhang of the template strand using its own internal RNA template.

DNA Polymerase Proofreading

The enzymatic ability of DNA polymerase to detect a mismatched base at the growing $3'$ end, pause, and excise it using intrinsic $3'\rightarrow 5'$ exonuclease activity before resuming polymerization.

Mismatch Repair

A post-replication surveillance system that detects base mismatches on newly synthesized unmethylated DNA, excises the segment containing the error, and fills the gap using the methylated parental strand as a template.

Thymine Dimer

A DNA lesion caused by ultraviolet (UV) radiation in which covalent bonds form between adjacent thymine bases on the same strand, producing a structural kink that halts replication and transcription.

Nucleotide Excision Repair (NER)

A general DNA repair pathway that recognizes bulky lesions (such as thymine dimers), cuts the damaged strand on either side of the defect, excises the oligonucleotide, and resynthesizes the gap with DNA polymerase and ligase.

Xeroderma Pigmentosum (XP)

A rare autosomal recessive human disease caused by mutations in nucleotide excision repair genes, leaving individuals unable to repair UV-induced DNA lesions and highly vulnerable to skin lesions and skin cancer.

Sanger Sequencing (Dideoxy Sequencing)

A DNA sequencing method that uses dideoxynucleoside triphosphates ($\text{ddNTPs}$) lacking a $3'\text{-OH}$ group to cause premature chain termination at specific base positions during in vitro polymerization.

Central Dogma

The principle formulated by Francis Crick stating that genetic information flows from DNA to RNA to protein, and that once sequence information reaches protein, it cannot flow back.

Codon

A sequence of three consecutive nucleotides in an mRNA molecule that specifies a particular amino acid or serves as a translational start or stop signal.

Open Reading Frame (ORF)

A continuous stretch of codons in an mRNA molecule that begins with a start codon ($\text{AUG}$), continues in a specific reading frame, and terminates at an in-frame stop codon.

Degenerate Code

The feature of the genetic code in which multiple different triplet codons can specify the same amino acid (all amino acids except two have redundant codons).

Missense Mutation

A point mutation (base-pair substitution) in a coding region that changes an mRNA codon such that it encodes a different amino acid.

Nonsense Mutation

A base-pair substitution in a coding sequence that converts an amino acid-specifying codon into a premature stop codon, terminating translation early.

Silent Mutation

A base-pair substitution within a protein-coding region that does not change the amino acid sequence of the resulting polypeptide due to the degeneracy of the genetic code.

Frameshift Mutation

The insertion or deletion of one or more base pairs (not in multiples of three) in a protein-coding sequence, shifting the translational reading frame and altering all downstream codons.

Sigma Factor

A bacterial protein subunit that binds core RNA polymerase to guide the holoenzyme to specific promoter sequences, such as the $-10$ and $-35$ boxes.

RNA Polymerase Holoenzyme

The fully functional prokaryotic transcription initiation complex composed of the core RNA polymerase enzyme together with a sigma factor.

-10 and -35 Boxes

Two conserved consensus sequence elements in bacterial promoters, located approximately 10 bases and 35 bases upstream of the $+1$ transcription start site, recognized by the sigma factor.

Exon

A transcribed region of a eukaryotic gene that is retained in the primary transcript during RNA splicing and forms part of the mature mRNA exported to the cytoplasm.

Intron

A non-coding intervening sequence in a eukaryotic structural gene that is transcribed into pre-mRNA but excised during RNA processing.

Spliceosome

A large nuclear ribonucleoprotein machine formed from small nuclear ribonucleoproteins (snRNPs) that recognizes specific splice sites to excise introns and ligate exons.

5' Cap

A modified 7-methylguanosine residue linked via an unusual $5'\text{-to-}5'$ triphosphate bridge to the $5'$ end of eukaryotic pre-mRNA, required for nuclear export, transcript stability, and ribosome binding.

Poly-A Tail

A non-templated stretch of 50 to 250 adenine nucleotides added post-transcriptionally to the cleaved $3'$ end of eukaryotic pre-mRNA by poly-A polymerase to facilitate nuclear export and cytosolic stability.

Polyribosome (Polysome)

A complex consisting of a single mRNA molecule simultaneously being translated by multiple ribosomes lined up along its length.

Transfer RNA (tRNA)

A small adaptor RNA molecule folded into a cloverleaf secondary structure and an L-shaped tertiary structure that carries a specific amino acid at its $3'$ CCA end and pairs with an mRNA codon via its anticodon.

Aminoacyl-tRNA Synthetase

An enzyme that charges a specific tRNA molecule by catalyzing the ATP-dependent covalent attachment of its corresponding amino acid to the tRNA's $2'$ or $3'\text{-OH}$ terminal group.

Wobble Hypothesis

Crick's proposal stating that non-standard base pairing is permitted at the third position of an mRNA codon (and the first position of the anticodon), allowing a single tRNA species to recognize multiple synonymous codons.

Shine-Dalgarno Sequence

A consensus ribosome-binding site located upstream of the start codon in bacterial mRNA that pairs with complementary rRNA in the small ribosomal subunit to properly align translation initiation.

N-Formylmethionine (f-Met)

The formylated amino acid carried by the initiator tRNA in bacteria that base-pairs with the $\text{AUG}$ start codon during translation initiation.

Translocation (Translation)

The GTP-dependent movement of the ribosome by three nucleotides along the mRNA, shifting the uncharged tRNA to the E site, the peptidyl-tRNA to the P site, and clearing the A site.

Release Factor

A protein that structurally mimics a tRNA and enters the ribosomal A site upon encountering a stop codon, catalyzing the hydrolysis of the ester bond linking the polypeptide to the P-site tRNA.

Operon

A functional genetic unit found predominantly in prokaryotes consisting of a cluster of related genes transcribed as a single polycistronic mRNA under the control of a single promoter and operator.

Polycistronic mRNA

A bacterial transcript that carries the coding sequences (cistrons) for two or more distinct proteins, each with its own ribosome-binding site and stop codon.

Inducer

A small effector molecule that binds to a transcriptional repressor or activator protein to stimulate expression of a target gene or operon.

Allolactose

A lactose conformational isomer generated by a side reaction of $\beta$-galactosidase that acts as the physiological inducer of the lac operon by binding the LacI repressor.

Catabolite Activator Protein (CAP)

A bacterial transcriptional activator that binds cyclic AMP (cAMP) when glucose levels are low and subsequently binds the CAP site upstream of the lac promoter to enhance RNA polymerase recruitment.

Catabolite Repression

A regulatory mechanism in E. coli where the presence of a preferred catabolite (glucose) lowers intracellular cAMP levels, preventing CAP binding and repressing transcription of alternative sugar operons.

Corepressor

A small effector molecule (such as tryptophan) that binds to an inactive aporepressor to activate it, allowing the repressor complex to bind the operator and block transcription.

Attenuation

A regulatory mechanism in bacterial amino acid biosynthetic operons (such as trp) in which the rate of translation of a leader peptide controls the formation of alternative mRNA secondary structures that either terminate or permit transcription.

Nucleosome

The basic repeating unit of eukaryotic chromatin, consisting of approximately 146 to 200 base pairs of DNA wound around an octamer of core histone proteins.

Histone Acetyltransferase (HAT)

An enzyme that transfers acetyl groups to amine groups on histone lysine residues, eliminating their positive charges and decondensing chromatin to promote gene expression.

Histone Deacetylase (HDAC)

An enzyme that removes acetyl groups from lysine residues on histones, restoring their positive charges and causing chromatin condensation and transcriptional repression.

Alternative Splicing

A post-transcriptional process in eukaryotes where different combinations of exons from a single pre-mRNA transcript are joined or skipped, generating multiple distinct protein isoforms from a single gene.

Enhancer

A eukaryotic regulatory DNA element located up to $100{,}000\text{ bp}$ away from the promoter that binds activator proteins to stimulate transcription.

Silencer

A eukaryotic DNA regulatory site that binds repressor proteins to downregulate or repress transcription of an associated gene.