Molecular Biology: Translation, DNA Mutation and Repair, and Chromosome Structure

Vocabulary practice flashcards covering translation machinery and phases, spontaneous and induced DNA mutations, repair pathways, chromatin compaction levels, chromosome organization, and epigenetic modifications.

Peptide Bond

A covalent bond formed during translation between the carboxyl ($\text{COOH}$) group of one amino acid and the amino ($\text{NH}_3$) group of another amino acid.

Aminoacyl (A) Site

The ribosomal site that binds incoming charged tRNAs whose anticodons match the exposed mRNA codon, bringing the next amino acid for polypeptide synthesis.

Peptidyl (P) Site

The ribosomal site that holds the tRNA attached to the growing polypeptide chain; also the only site that directly binds the charged initiator tRNA during translation initiation.

Exit (E) Site

The ribosomal site where an uncharged tRNA briefly pauses before dissociating from the ribosome after transferring its amino acid to the growing polypeptide chain.

Svedberg (S) Unit

A non-additive unit of sedimentation rate used to measure ribosomal subunits, determined by molecular size, shape, and hydration during ultracentrifugation.

Synonymous Codons

Different codons that encode the same amino acid in the degenerate genetic code; all amino acids except methionine and tryptophan are specified by at least two such codons.

Isoaccepting tRNAs

Transfer RNA molecules that possess distinct anticodon sequences but are charged with and carry the same specific amino acid.

Third-Base Wobble

The relaxation of strict complementary base-pairing rules at the $3'$ nucleotide position of an mRNA codon, enabling a single tRNA anticodon to pair with multiple codons provided purine-pyrimidine pairing is preserved.

Inosine

A modified, deaminated adenosine nucleotide present in some tRNA anticodons that structurally resembles guanosine and can base-pair with adenine, uracil, or cytosine (but not guanine).

Aminoacyl-tRNA Synthetase

One of 20 distinct enzymes that covalently attaches the appropriate amino acid to its corresponding tRNA molecule via an energy-requiring charging process.

Shine-Dalgarno Sequence

An adenine/guanine-rich consensus sequence located $3\text{ to }9\text{ nucleotides}$ upstream of the start codon in bacterial $5'\text{ UTRs}$ that pairs with 16S rRNA to position the start codon at the P site.

Kozak Sequence

A eukaryotic consensus sequence ($5'\text{-ACCAUGG-}3'$) recognized by the scanning $40\text{S}$ small ribosomal subunit to identify the correct start codon.

EF-Tu

A bacterial elongation factor protein that binds a charged tRNA alongside GTP, escorting the tRNA to the ribosomal A site and releasing upon GTP hydrolysis after correct codon-anticodon pairing.

EF-G

A bacterial elongation factor that hydrolyzes GTP to translocate the ribosome by exactly one codon ($3\text{ nucleotides}$) toward the $3'$ end of the mRNA.

Release Factor (RF)

A protein (such as eRF1 in eukaryotes, or RF1 and RF2 in bacteria) that recognizes a stop codon in the ribosomal A site and catalyzes the release of the newly synthesized polypeptide.

Polycistronic mRNA

A bacterial mRNA transcript carrying multiple distinct polypeptide-coding segments (cistrons), each containing its own Shine-Dalgarno sequence, start codon, and stop codon separated by intercistronic spacers.

Signal Sequence

A stretch of the first $15\text{ to }20$ amino acids at the N-terminal end of a nascent polypeptide that directs the protein to its correct subcellular destination.

Mutation Rate

The measured frequency of mutational events occurring in a given gene per generation, generally ranging between $1 \times 10^{-9}$ and $1 \times 10^{-4}$.

Hotspots of Mutation

Specific genes or genomic regions that exhibit a significantly higher rate of mutation than the average baseline rate for an organism.

Silent Mutation

A base-pair substitution within a protein-coding sequence that alters a codon to a synonymous codon without changing the encoded amino acid.

Missense Mutation

A base-pair substitution within a protein-coding sequence that alters a codon so that it specifies a different amino acid.

Nonsense Mutation

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

Frameshift Mutation

The insertion or deletion of one or more base pairs in a quantity not divisible by $3$, shifting the translational reading frame and altering all downstream codons.

Strand Slippage

A replication error at repetitive DNA tracts where DNA polymerase transiently dissociates, enabling hairpin formation on the new or template strand and resulting in repeat expansions or contractions.

Tautomeric Shift

A temporary, spontaneous structural alteration in a DNA base that changes its hydrogen bonding properties, causing mispairing during replication and producing transition mutations.

Depurination

A spontaneous nucleotide lesion characterized by the breakage of the glycosidic bond and loss of a purine base (adenine or guanine), generating an apurinic site.

Deamination

The loss of an amino group ($\text{NH}_2$) from a nucleotide base; converts cytosine into uracil, or methylated cytosine (5-meC) into thymine.

Base Analog

A chemical mutagen structurally similar to normal nitrogenous bases (such as 5-bromodeoxyuridine/BrdU) that DNA polymerase incorporates into replicating DNA, subsequently causing transition mutations.

Alkylating Agent

A chemical mutagen (such as ethyl methanesulfonate/EMS) that attaches alkyl groups like methyl or ethyl adducts to nucleotide bases, causing helix distortion and replication mispairing.

Intercalating Agent

A planar chemical compound (such as proflavin or acridine orange) that wedges between stacked DNA base pairs, interfering with topoisomerase II and inducing frameshift mutations.

Thymine Dimer

A UV-induced photoproduct characterized by two covalent bonds formed between adjacent thymine residues on the same strand, causing distortion of the DNA double helix.

Nucleotide Base Excision Repair (BER)

A cellular DNA repair mechanism wherein DNA glycosylases recognize and cleave damaged bases, followed by endonuclease excision of the remainder of the nucleotide, DNA polymerase filling, and ligase sealing.

Nucleotide Excision Repair (NER)

A repair pathway that removes helix-distorting DNA damage (such as UV-induced pyrimidine dimers or bulky chemical adducts) by excising a multi-nucleotide oligonucleotide fragment around the lesion.

p53

A tumor suppressor transcription factor stabilized by ATM-dependent checkpoint kinases following DNA damage; it upregulates p21 to arrest the cell cycle or BAX to induce apoptosis.

Nonhomologous End Joining (NHEJ)

An error-prone double-strand break repair mechanism active during the G1 phase of the cell cycle that trims and ligates broken chromosome ends without a homologous template.

Synthesis-Dependent Strand Annealing (SDSA)

An error-free double-strand break repair mechanism operating after S phase that uses Rad51 to mediate strand invasion of an intact sister chromatid, forming a D loop to template accurate DNA synthesis.

Chromatin

The eukaryotic nuclear complex of linear genomic DNA combined with histone and nonhistone proteins that organizes and compacts genetic material.

Histones

Five small, basic, positively charged proteins (H1, H2A, H2B, H3, and H4) that bind tightly to negatively charged DNA to facilitate compaction into nucleosomes.

Nucleosome Core Particle

The fundamental unit of chromatin compaction, consisting of an octamer of two H2A/H2B dimers and two H3/H4 dimers wrapped by approximately $146\,\text{bp}$ of core DNA.

10 nm Fiber

The 'beads-on-a-string' chromatin conformation formed by nucleosomes connected by $40\text{ to }50\,\text{bp}$ of linker DNA, compacting unwound DNA approximately 7-fold.

30 nm Fiber (Solenoid)

A higher-order cylindrical chromatin structure formed when histone H1 links adjacent nucleosomes together, packing approximately $6\text{ to }8$ nucleosomes per helical turn.

Matrix Attachment Regions (MARs)

Repetitive, AT-rich nonhistone anchor sequences (ATC sequences) that affix $20{,}000\text{ to }100{,}000\,\text{bp}$ loops of the 30 nm chromatin fiber to the nuclear chromosome scaffold.

Condensin

A protein complex that relocates from the cytoplasm into the nucleus during prophase to compact the radial chromatin loops into dense metaphase chromosomes.

Chromosome Territory

A dedicated, non-overlapping 3D region of the interphase nucleus occupied by an individual chromosome anchored by its centromere.

Interchromosomal Domains

Chromatin-free channels separating adjacent chromosome territories that serve as conduits for the movement of RNA transcripts, enzymes, and regulatory factors.

Giemsa (G) Banding

A cytogenetic staining method that produces a reproducible pattern of approximately 300 alternating light and dark bands across human metaphase chromosomes for identification and karyotyping.

Euchromatin

Relatively uncondensed, lightly staining chromatin containing actively transcribed genes located away from centromeres and telomeres.

Heterochromatin

Highly compacted, darkly staining chromatin that contains few expressed genes and is predominantly composed of repetitive sequences.

Constitutive Heterochromatin

Chromatin regions (such as centromeres and telomeres) that remain permanently condensed, repetitive, and transcriptionally silenced across all cell types.

Facultative Heterochromatin

Chromatin whose degree of condensation varies between tissues or developmental stages, allowing transcription when decondensed (such as the inactive mammalian X chromosome).

CENP-A

A specialized histone H3 variant characterized by an elongated N-terminal tail found at centromeric nucleosomes, essential for the recruitment and binding of kinetochore proteins.

Position Effect

The repression or alteration of a gene's transcriptional expression resulting from its chromosomal relocation into or adjacent to a region of heterochromatin.

Epigenetics

The study of heritable changes in gene expression and cellular phenotype that take place without alterations to the underlying DNA nucleotide sequence.

Bivalent Domain

A promoter chromatin signature found in pluripotent stem cells featuring both activating ($\text{H3K4me3}$) and repressing ($\text{H3K27me3}$) histone methylation marks on the same nucleosome, keeping developmental genes poised for expression.

Polycomb Repressive Complex 2 (PRC2)

A four-subunit protein complex containing Ezh1 and Ezh2 that establishes epigenetic gene silencing via trimethylation of histone H3 at lysine 27 ($\text{H3K27me3}$).