The Process of Gene Expression

Comprehensive vocabulary flashcards covering the process of gene expression, transcription, translation, and protein quality control.

Continuous (Genetic Code)

Triplet codons are uninterrupted with no breaks between them (commaless), and the order is colinear.

Unambiguous (Genetic Code)

A feature of the genetic code where each individual codon specifies only a single amino acid.

Degenerate (Genetic Code)

A feature of the genetic code where amino acids can be associated with multiple different codons.

Nonoverlapping (Genetic Code)

In mRNA, each individual nucleotide is only part of one codon during an individual translation event.

Universal (Genetic Code)

Generally, all life on earth uses the same genetic code, with some exceptions found in mitochondrial codes.

RNA Editing

A colinear exception where the nature of a codon is changed, such as the deamination of Cytosine to Uracil; also an example of Epigenetics.

DNA-dependent RNA polymerase

The updated enzyme name for an enzyme that uses a DNA template to produce an RNA polymer product.

Reverse Transcription

An exception to the Central Dogma where an RNA template is used to make DNA, utilizing an RNA-dependent DNA polymerase.

TATA Binding Protein (TBP)

A component of TFIID that recognizes the TATA box and distorts the DNA helix during transcription initiation.

TFIIH

A general transcription factor complex containing a helicase (XPB) to create the transcription bubble and a kinase to phosphorylate the C-terminal domain of RNA Pol II.

Mediator

A complex in eukaryotes that holds pieces together and interacts with activator proteins to ensure transcription begins.

RNA Polymerase I

The specific RNA polymerase responsible for transcribing ribosomal RNA ($rRNA$).

RNA Polymerase II

The specific RNA polymerase responsible for transcribing messenger RNA ($mRNA$) and most other noncoding RNAs.

RNA Polymerase III

The specific RNA polymerase responsible for transcribing transfer RNA ($tRNA$) and some other small RNAs.

Promoter-Proximal Pausing

A regulatory step where RNA Pol II pauses after transcribing $20-60$ nucleotides, induced by NELF and maintained by DSIF.

Positive Transcription Elongation Factor b (P-TEFb)

A kinase that releases Promoter-Proximal Pausing by phosphorylating the C-terminal domain of RNA Pol II and the factors DSIF/NELF.

FACT (Facilitates Chromosome Transcription)

A chromosome remodeling complex composed of SPT16 and SSRP1 that removes histones (specifically H3/H4 dimers) ahead of the transcribing polymerase.

Type I Topoisomerase

An enzyme (e.g., TOP1, TOP3$\beta$) that nicks one DNA strand to "unwind" helical stress during transcription.

Type II Topoisomerase

An enzyme (e.g., TOP2$\alpha$, TOP2$\beta$) that opens two DNA strands to "untangle" DNA during transcription.

Poly(ADP-ribose) Polymerases (PARPs)

Master regulators like PARP1 that add ADP-ribose to histones and other proteins to coordinate the binding/removal of factors from the elongation complex.

Torpedo Model

A model of eukaryotic transcription termination where the exonuclease XRN2 chews back RNA and kicks off RNA Pol II upon collision.

Allosteric Model

A model of eukaryotic transcription termination where the PolyA tail signals RNA Pol II to change shape and fall off the DNA.

5' Cap

An upside down and backwards Guanine with an extra methyl group at the 5' end of RNA that protects against nucleases and directs nuclear export.

Group I Introns

Self-catalyzed (ribozyme) introns found in prokaryotes, eukaryotes, and organelles that yield linear or circularized introns after removal.

Group II Introns

Self-catalyzed ribozymes that create lariat structures; they are considered precursors to spliceosomal introns.

Spliceosome

A ribozyme mixture of RNAs and proteins that removes introns in eukaryotes, creating a lariat structure.

Alternative Splicing

A process of picking and choosing which exons to include in a mature mRNA to increase genetic diversity without changing the DNA sequence.

Poly-A Polymerase (PAP)

The enzyme responsible for adding approximately $200-250$ Adenines to the 3' end of an mRNA.

Small Nuclear RNAs (snRNAs)

Mid-range sized noncoding RNAs that function as part of the spliceosome.

Small Nucleolar RNAs (snoRNAs)

Mid-range sized RNAs that guide chemical modifications of other RNAs, such as the conversion of uridines to pseudouridines in rRNAs.

MicroRNAs (miRNAs)

Small noncoding RNAs that inhibit translation; they typically feature a hairpin shape with a bulge indicating an imperfect sequence match.

Small Interfering RNAs (siRNAs)

Small dsRNAs that block translation by degrading RNAs or block transcription by promoting heterochromatin formation.

Piwi-interacting RNAs (piRNAs)

Small RNAs that associate with PIWI proteins to protect the germ line by silencing transposons via DNA methylation.

lncRNA Signal Archetype

A long noncoding RNA that indicates transcriptional activity; an example is Xist, which coats and inactivates the X chromosome.

lncRNA Decoy Archetype

A long noncoding RNA that fools DNA-binding regulatory proteins, such as Gas5 binding to the glucocorticoid receptor.

lncRNA Guide Archetype

A long noncoding RNA that directs the localization of protein complexes, such as HOTAIR directing PRC2.

lncRNA Scaffold Archetype

A long noncoding RNA that physically connects at least two proteins to hold elements in proximity.

Ribozyme

A complex of RNA and protein where the RNA component performs the catalytic function, such as the ribosome or the spliceosome.

Aminoacyl-tRNA Synthetase

A specific enzyme that links the appropriate amino acid to its corresponding tRNA via a high-energy bond.

Wobble Position

The flexibility in base-pairing at the third position of a codon, allowing fewer tRNAs to be needed than there are codons in the genetic table.

eIF4F

A translation initiation complex composed of eIF4E, eIF4A, and eIF4G that binds to the mRNA 5' cap.

Nonsense Mediated Decay (NMD)

A quality control mechanism that detects and degrades mRNAs containing premature stop codons, often involving UPF and SMG proteins.

Chaperone Proteins

Proteins such as Hsp60 and Hsp70 that assist newly translated polypeptides in folding correctly into their functional 3-D shapes.

Unfolded Protein Response (UPR)

A eukaryotic stress response triggered by misfolded proteins that involves pathways like IRE1, ATF6, and PERK to resolve the stress.

PERK Pathway

A UPR pathway that phosphorylates eIF2 to decrease general translation while increasing the production of ER chaperones and pro-apoptosis factors.