DNA Replication, Gene Expression, and Mutation Repair

Vocabulary practice flashcards covering Chapter 8: DNA replication, transcription, translation, ribosomal structures, mutations, and DNA repair mechanisms.

Gene

A segment of transcribed DNA, noting that not all transcribed genes make a protein.

Replication

The biological information flow process wherein DNA directs the synthesis of new DNA ($\text{DNA} \rightarrow \text{DNA}$).

Transcription

The biological information flow process in which a DNA sequence is copied into RNA ($\text{DNA} \rightarrow \text{RNA}$).

Translation

The biological information flow process in which the genetic code in an RNA transcript is converted into a polypeptide or protein ($\text{RNA} \rightarrow \text{protein}$).

Messenger RNA (mRNA)

Coding RNA molecules ranging from approximately $500$ to $10{,}000$ nucleotides that are translated into proteins.

Transfer RNA (tRNA)

Adaptor RNA molecules of approximately $75\text{--}100$ nucleotides that fold into a cloverleaf structure with hairpins, become charged with specific amino acids, and carry anticodons to read mRNA codons during translation.

Ribosomal RNA (rRNA)

Structural and enzymatic RNA components of ribosomes, measuring approximately $1{,}500\text{--}1{,}900$ nucleotides in the small subunit and $2{,}900\text{--}4{,}700$ nucleotides in the large subunit.

Micro RNA (miRNA)

Small non-coding RNA molecules of less than $100$ nucleotides ($<100$ nucleotides) that carry out various regulatory functions in the cell.

Promoter

A specific sequence of DNA upstream of a gene (where $+1$ indicates the transcription start site) that directs the binding of RNA polymerase and initiation factors.

Sigma Factor

A bacterial protein that binds to the RNA polymerase core enzyme to form the holoenzyme and direct it to the promoter to initiate transcription; different sigma factors are transcribed at different times as a mechanism of gene expression control.

Operon

A cluster of multiple genes transcribed together under the control of a single promoter into one continuous transcript, common in bacteria.

Post-Transcriptional Processing

A three-step eukaryotic maturation process for pre-mRNA consisting of adding a $5'$ cap (7-methylguanosine), adding a poly(A) tail to the $3'$ end, and splicing out introns while joining exons together.

Degenerate Code

A property of the genetic code wherein multiple different three-nucleotide codons can specify the same amino acid ($61$ codons encoding $20$ amino acids).

Anticodon

A three-nucleotide sequence on a tRNA molecule that base-pairs complementarily with a corresponding three-letter codon on an mRNA transcript.

Aminoacyl-tRNA Synthetase

An enzyme that attaches the correct, specific amino acid to the $3'$ end of its corresponding tRNA, thereby charging the tRNA for translation.

16S rRNA

The structural ribosomal RNA component of the bacterial small ($30\text{S}$) subunit that base-pairs with the Shine-Dalgarno sequence and serves as a primary gene marker used to identify bacteria.

Shine-Dalgarno Sequence (Ribosome Binding Site / RBS)

A specific nucleotide sequence upstream of the start codon on bacterial mRNA that base-pairs with the 16S rRNA of the $30\text{S}$ subunit to properly position the ribosome for translation initiation.

Open Reading Frame (ORF)

A continuous stretch of codons on an mRNA beginning with a start codon (typically AUG) and ending with a stop codon that can be translated into a polypeptide.

A Site (Aminoacyl Site)

The ribosomal binding site where each incoming charged tRNA carrying its specified amino acid first enters during translation elongation.

P Site (Peptidyl Site)

The middle site of the ribosome where the tRNA carrying the growing polypeptide chain resides and peptide bond formation occurs.

E Site (Exit Site)

The ribosomal site through which an uncharged tRNA exits the ribosome after transferring its amino acid to the growing peptide chain.

Polycistronic mRNA

A single mRNA transcript that carries the coding sequences for multiple structural genes, each equipped with its own Shine-Dalgarno sequence, start codon, and stop codon.

Chaperone Protein

A specialized protein that assists newly synthesized polypeptide chains in folding properly into their functional three-dimensional conformations.

Signal Peptide

A sequence within a synthesized protein that functions as an address label telling the cell where the protein needs to be trafficked or transported.

Proofreading

The intrinsic error-detection and correction activity of DNA polymerase that identifies and removes mismatched bases during replication, limiting spontaneous mutations to approximately $1\text{ in }1\text{ billion}$ bases.

Silent Mutation

A point mutation (frequently in the 3rd codon position) that alters a nucleotide without changing the specified amino acid or resulting protein sequence.

Missense Mutation

A point mutation that replaces a single nucleotide in a codon, resulting in the substitution of a different amino acid in the encoded protein.

Nonsense Mutation

A point mutation that converts an amino acid-specifying codon into a stop codon, terminating protein synthesis prematurely.

Frameshift Mutation (Indel)

An insertion or deletion of base pairs that shifts the translational reading frame, altering all downstream codons and yielding an altered protein.

Chromosomal Inversion

A large-scale chromosomal rearrangement in which a segment of DNA is cleaved at two breakpoints, inverted $180^\circ$, and reinserted into the chromosome.

Chromosomal Translocation

A large-scale mutation where a broken end piece of a chromosome is swapped or joined with another non-homologous chromosome.

Mismatch Repair

A bacterial DNA repair pathway involving MutS, MutL, and MutH that identifies mispaired bases and selectively excises the newly synthesized strand based on the absence of parental methylation tags.

Photolyase

A DNA repair enzyme that binds to thymine dimers caused by ultraviolet (UV) radiation and cleaves the covalent bonds linking the adjacent thymines.